# Developing-Heart-Local-Improved - Atac Preprocessing

**Pages:** 8

---

## Notebook

**URL:** http://127.0.0.1:9020/notebooks_html/Fig1_General_processing/ATAC/ATAC_preprocess/ArchR_no2_global_CreateArchRproject_Filtering_Clustering.html

**Contents:**
- Prepare Arrow files¶
- Create an ArchR Project¶
- Plotting¶
- Add fine-grained cell type annotation from RNA data¶
- Dimensionality reduction with ArchR¶
  - Iterative Latent Semantic Indexing (LSI)¶
  - Batch Effect Correction wtih Harmony¶
- Clustering¶
  - create a cluster confusion matrix¶
- Single-cell Embeddings¶
  - UMAP¶
- Save project¶
- Save cell index¶

Ref: https://www.archrproject.com/bookdown/creating-an-archrproject-1.html

**Examples:**

Example 1 (unknown):
```unknown
library(ArchR)
library(tidyverse)
```

Example 2 (javascript):
```javascript
/ |
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            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    

ArchR : Version 1.0.2
For more information see our website : www.ArchRProject.com
If you encounter a bug please report : https://github.com/GreenleafLab/ArchR/issues

Loading Required Packages...

	Loading Package : grid v4.0.4

	Loading Package : gridExtra v2.3

	Loading Package : gtools v3.9.3

	Loading Package : gtable v0.3.0

	Loading Package : ggplot2 v3.4.0

	Loading Package : magrittr v2.0.3

	Loading Package : plyr v1.8.8

	Loading Package : stringr v1.4.0

	Loading Package : data.table v1.14.4

	Loading Package : matrixStats v0.62.0

	Loading Package : S4Vectors v0.28.1

	Loading Package : GenomicRanges v1.42.0

	Loading Package : BiocGenerics v0.36.1

	Loading Package : Matrix v1.3.2

	Loading Package : Rcpp v1.0.9

	Loading Package : SummarizedExperiment v1.20.0

	Loading Package : rhdf5 v2.34.0

Warning message in system("timedatectl", intern = TRUE):
“running command 'timedatectl' had status 1”
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ tibble  3.1.8      ✔ purrr   0.3.4 
✔ tidyr   1.2.1      ✔ dplyr   1.0.10
✔ readr   2.1.3      ✔ forcats 0.5.1 
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::arrange()         masks plyr::arrange()
✖ dplyr::between()         masks data.table::between()
✖ dplyr::collapse()        masks IRanges::collapse()
✖ dplyr::combine()         masks Biobase::combine(), BiocGenerics::combine(), gridExtra::combine()
✖ purrr::compact()         masks plyr::compact()
✖ dplyr::count()           masks matrixStats::count(), plyr::count()
✖ dplyr::desc()            masks IRanges::desc(), plyr::desc()
✖ tidyr::expand()          masks Matrix::expand(), S4Vectors::expand()
✖ tidyr::extract()         masks magrittr::extract()
✖ dplyr::failwith()        masks plyr::failwith()
✖ dplyr::filter()          masks stats::filter()
✖ dplyr::first()           masks S4Vectors::first(), data.table::first()
✖ dplyr::id()              masks plyr::id()
✖ dplyr::lag()             masks stats::lag()
✖ dplyr::last()            masks data.table::last()
✖ dplyr::mutate()          masks plyr::mutate()
✖ tidyr::pack()            masks Matrix::pack()
✖ BiocGenerics::Position() masks ggplot2::Position(), base::Position()
✖ purrr::reduce()          masks GenomicRanges::reduce(), IRanges::reduce()
✖ dplyr::rename()          masks S4Vectors::rename(), plyr::rename()
✖ purrr::set_names()       masks magrittr::set_names()
✖ dplyr::slice()           masks IRanges::slice()
✖ dplyr::summarise()       masks plyr::summarise()
✖ dplyr::summarize()       masks plyr::summarize()
✖ purrr::transpose()       masks data.table::transpose()
✖ tidyr::unpack()          masks Matrix::unpack()
```

Example 3 (unknown):
```unknown
# before starting a project we must set the ArchRGenome and default threads for parallelization.
# Setting default genome to Hg38.
addArchRGenome("hg38")
```

Example 4 (unknown):
```unknown
Setting default genome to Hg38.
```

Example 5 (unknown):
```unknown
# Setting default number of Parallel threads to 16
addArchRThreads(threads = 10)
```

Example 6 (unknown):
```unknown
Setting default number of Parallel threads to 10.
```

Example 7 (python):
```python
# read in rna metadata
obs = read.csv('/nfs/team205/heart/anndata_objects/Foetal/Feb28ObjectRaw.obs.csv',row.names=1)

# select modality (multiome)
print(table(obs$kit_10x))
obs = obs %>% filter(kit_10x == "Multiome-v1")

# select columns
obs = obs %>% select('sangerID', 'combinedID', 'donor', 
       'facility', 'cell_or_nuclei', 'modality', 'kit_10x', 
       'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts',
       'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts',
       'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt',
       'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo',
       'pct_counts_ribo', 'HB_score', 'donor_by_library.prep','multiplexed',
        'batch_key','region','FACSgate','sex','week','trimester',
                     'fine_grain','mid_grain','coarse_grain',
                     'heart_or_greatvessels','cycling','S_score','G2M_score','phase','stress_score','hb1_score')

print(dim(obs))
head(obs)
```

Example 8 (unknown):
```unknown
3prime-v3   5prime-v2 Multiome-v1 
      39718       46610      211145 
[1] 211145     41
```

Example 9 (unknown):
```unknown
# make arrow file list using combinedID
ArrowFiles = paste0(unique(obs$combinedID),'.arrow')
length(ArrowFiles)
ArrowFiles
```

Example 10 (unknown):
```unknown
proj <- ArchRProject(
  ArrowFiles = ArrowFiles, 
  outputDirectory = "project_output",
  copyArrows = FALSE #This is recommened so that if you modify the Arrow files you have an original copy for later usage.
)
# copyArrows = FALSE since copy Arrows will be created when we save project file
```

Example 11 (python):
```python
Using GeneAnnotation set by addArchRGenome(Hg38)!

Using GeneAnnotation set by addArchRGenome(Hg38)!

Validating Arrows...

Getting SampleNames...



Getting Cell Metadata...



Merging Cell Metadata...

Initializing ArchRProject...


                                                   / |
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                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 12 (unknown):
```unknown
___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 13 (unknown):
```unknown
class: ArchRProject 
outputDirectory: /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output 
samples(37): BHF_F_Hea11064670_BHF_F_Hea11031823
  BHF_F_Hea11064671_BHF_F_Hea11031824 ...
  HCAHeartST13386009_HCAHeartST13303419
  HCAHeartST13386010_HCAHeartST13303420
sampleColData names(1): ArrowFiles
cellColData names(13): Sample TSSEnrichment ... nDiFrags BlacklistRatio
numberOfCells(1): 497607
medianTSS(1): 11.159
medianFrags(1): 8628
```

Example 14 (unknown):
```unknown
colnames(proj@cellColData)
```

Example 15 (unknown):
```unknown
paste0("Memory Size = ", round(object.size(proj) / 10^6, 3), " MB")
```

Example 16 (unknown):
```unknown
# getAvailableMatrices(proj)
```

Example 17 (unknown):
```unknown
# TSS enrichment score
p1 <- plotGroups(
    ArchRProj = proj, 
    groupBy = "Sample", 
    colorBy = "cellColData", 
    name = "TSSEnrichment",
    plotAs = "violin",
    alpha = 0.4,
    addBoxPlot = TRUE
   )
p1
```

Example 18 (unknown):
```unknown
Length of unique values greater than palette, interpolating..

1
```

Example 19 (unknown):
```unknown
# log10(unique nuclear fragments)
p2 <- plotGroups(
    ArchRProj = proj, 
    groupBy = "Sample", 
    colorBy = "cellColData", 
    name = "log10(nFrags)",
    plotAs = "violin",
    alpha = 0.4,
    addBoxPlot = TRUE
   )
p2
```

Example 20 (unknown):
```unknown
Length of unique values greater than palette, interpolating..

1
```

Example 21 (unknown):
```unknown
plotPDF(p1,p2, name = "QC-Sample-Statistics.pdf", ArchRProj = proj, addDOC = FALSE, width = 8, height = 5)
```

Example 22 (unknown):
```unknown
Plotting Ggplot!

Plotting Ggplot!
```

Example 23 (python):
```python
# change cell names to match with .obs metadata
proj$cellNames_mod = gsub("#", "_", proj$cellNames)
proj$cellNames_mod[1:10]
```

Example 24 (python):
```python
# keep cellColData dataframe for later use
cellColData_prefilter = proj@cellColData

# select shared cells between RNA and ATAC
shared_cells = intersect(proj$cellNames_mod, rownames(obs))
length(shared_cells)

# select shared cells fromr the ArchR pobject
idxSample <- BiocGenerics::which(proj$cellNames_mod %in% shared_cells)
cellsSample <- proj$cellNames[idxSample]
proj = proj[cellsSample, ]
proj

# select shared cells fromr the .obs metadata
obs = obs[proj$cellNames_mod, ]
dim(obs)
```

Example 25 (unknown):
```unknown
___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 26 (unknown):
```unknown
class: ArchRProject 
outputDirectory: /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output 
samples(37): BHF_F_Hea11064670_BHF_F_Hea11031823
  BHF_F_Hea11064671_BHF_F_Hea11031824 ...
  HCAHeartST13386009_HCAHeartST13303419
  HCAHeartST13386010_HCAHeartST13303420
sampleColData names(1): ArrowFiles
cellColData names(14): Sample TSSEnrichment ... BlacklistRatio
  cellNames_mod
numberOfCells(1): 167022
medianTSS(1): 11.614
medianFrags(1): 10338.5
```

Example 27 (python):
```python
# add metadata
for (c in colnames(obs)){
    proj = addCellColData(ArchRProj = proj, data = obs[[c]], cells = proj$cellNames, name = c)
}
```

Example 28 (unknown):
```unknown
table(proj$coarse_grain)
```

Example 29 (unknown):
```unknown
Cardiomyocytes    Endothelium     Epicardium     Leukocytes    Mesenchymal 
         53512           8859           1554          21340          78731 
        Neural 
          3026
```

Example 30 (unknown):
```unknown
table(proj$fine_grain)
```

Example 31 (unknown):
```unknown
AtrialCardiomyocytesCycling 
                                      1597 
                  AtrialCardiomyocytesLeft 
                                      4777 
                 AtrialCardiomyocytesRight 
                                      8187 
        AtrioventricularNodeCardiomyocytes 
                                       643 
                                    BCells 
                                      1369 
                            BCellsMS4A1pos 
                                      2559 
                           ChromaffinCells 
                                       112 
          CoronaryArterialEndothelialCells 
                                       353 
         CoronaryCapillaryEndothelialCells 
                                      2449 
                         CoronaryPericytes 
                                       688 
                 CoronarySmoothMuscleCells 
                                       415 
            CoronaryVenousEndothelialCells 
                                       539 
      CoronaryVesselAdventitialFibroblasts 
                                      1613 
                      DendriticCellsMature 
                                       156 
                       DendriticCellsType1 
                                       425 
         DuctusArteriosusSmoothMuscleCells 
                                      1159 
                          EndocardialCells 
                                      2690 
                   EndocardialCushionCells 
                                       224 
                    EpicardiumDerivedCells 
                                       340 
         GreatVesselAdventitialFibroblasts 
                                     31525 
       GreatVesselArterialEndothelialCells 
                                       929 
              GreatVesselSmoothMuscleCells 
                                     14126 
         GreatVesselVenousEndothelialCells 
                                       207 
                       InnateLymphoidCells 
                                       547 
                 LymphaticEndothelialCells 
                                      1282 
       LymphNodeFibroblasticReticularCells 
                                       969 
                        MacrophagesATF3pos 
                                       611 
                      MacrophagesCX3CR1pos 
                                       551 
                       MacrophagesLYVE1pos 
                                      4157 
                       MacrophagesTIMD4pos 
                                       303 
                                 MastCells 
                                       190 
                            Megakaryocytes 
                                       118 
                MesothelialEpicardialCells 
                                      1214 
                      MonocyteDerivedCells 
                                       386 
                                 Monocytes 
                                       117 
                           MonocytesMPOpos 
                                        34 
        MyocardialInterstitialFibroblasts1 
                                      7671 
        MyocardialInterstitialFibroblasts2 
                                      5123 
                            Myofibroblasts 
                                      3214 
                        NaturalKillerCells 
                                      1406 
                          NeuronPrecursors 
                                       371 
                     ParaympatheticNeurons 
                                       264 
                         PericardialCells1 
                                      8967 
                         PericardialCells2 
                                       187 
                         PericardialCells3 
                                      1040 
                PlasmacytoidDendriticCells 
                                       430 
                                 ProBCells 
                                       459 
                     SchwannCellPrecursors 
                                       759 
                              SchwannCells 
                                      1166 
              SinoatrialNodeCardiomyocytes 
                                       738 
                        SympatheticNeurons 
                                       354 
                              TCellsCD4pos 
                                      4251 
                              TCellsCD8pos 
                                      1810 
                               TregsCD4pos 
                                      1461 
                     ValveEndothelialCells 
                                       186 
                    ValveInterstitialCells 
                                      2034 
          VentricularCardiomyocytesCycling 
                                      4977 
      VentricularCardiomyocytesLeftCompact 
                                     11397 
 VentricularCardiomyocytesLeftTrabeculated 
                                      5054 
     VentricularCardiomyocytesRightCompact 
                                     12008 
VentricularCardiomyocytesRightTrabeculated 
                                      2269 
         VentricularConductionSystemDistal 
                                       531 
       VentricularConductionSystemProximal 
                                      1334
```

Example 32 (unknown):
```unknown
proj <- addIterativeLSI(
    ArchRProj = proj,
    useMatrix = "TileMatrix", 
    name = "IterativeLSI", 
    iterations = 2, 
    clusterParams = list( #See Seurat::FindClusters
        resolution = c(0.2), 
        sampleCells = 10000, 
        n.start = 10
    ), 
    varFeatures = 25000, 
    dimsToUse = 1:30
)
```

Example 33 (unknown):
```unknown
Checking Inputs...

ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-1c3a2773b85e-Date-2023-03-09_Time-10-33-14.log
If there is an issue, please report to github with logFile!

2023-03-09 10:33:16 : Computing Total Across All Features, 0.028 mins elapsed.

2023-03-09 10:34:39 : Computing Top Features, 1.395 mins elapsed.

###########
2023-03-09 10:34:42 : Running LSI (1 of 2) on Top Features, 1.451 mins elapsed.
###########

2023-03-09 10:34:42 : Sampling Cells (N = 10017) for Estimated LSI, 1.455 mins elapsed.

2023-03-09 10:34:42 : Creating Sampled Partial Matrix, 1.455 mins elapsed.

2023-03-09 10:38:30 : Computing Estimated LSI (projectAll = FALSE), 5.252 mins elapsed.

2023-03-09 10:39:00 : Identifying Clusters, 5.756 mins elapsed.

2023-03-09 10:39:26 : Identified 6 Clusters, 6.194 mins elapsed.

2023-03-09 10:39:27 : Saving LSI Iteration, 6.195 mins elapsed.

Length of unique values greater than palette, interpolating..

2023-03-09 10:39:54 : Creating Cluster Matrix on the total Group Features, 6.661 mins elapsed.

2023-03-09 10:41:01 : Computing Variable Features, 7.777 mins elapsed.

###########
2023-03-09 10:41:02 : Running LSI (2 of 2) on Variable Features, 7.78 mins elapsed.
###########

2023-03-09 10:41:02 : Creating Partial Matrix, 7.782 mins elapsed.

2023-03-09 10:45:38 : Computing LSI, 12.388 mins elapsed.

2023-03-09 10:49:34 : Finished Running IterativeLSI, 16.324 mins elapsed.
```

Example 34 (unknown):
```unknown
proj <- addHarmony(
    ArchRProj = proj,
    reducedDims = "IterativeLSI",
    name = "Harmony",
    groupBy = "batch_key"
)
```

Example 35 (unknown):
```unknown
Warning message:
“Quick-TRANSfer stage steps exceeded maximum (= 8351100)”
Warning message:
“Quick-TRANSfer stage steps exceeded maximum (= 8351100)”
Warning message:
“Quick-TRANSfer stage steps exceeded maximum (= 8351100)”
Warning message:
“Quick-TRANSfer stage steps exceeded maximum (= 8351100)”
Harmony 1/10

Harmony 2/10

Harmony 3/10

Harmony converged after 3 iterations
```

Example 36 (unknown):
```unknown
table(proj$batch_key)
```

Example 37 (unknown):
```unknown
C104_Nuclei_Multiome-v1   C82_Nuclei_Multiome-v1   C85_Nuclei_Multiome-v1 
                    2068                      350                     2218 
  C87_Nuclei_Multiome-v1   C92_Nuclei_Multiome-v1   C98_Nuclei_Multiome-v1 
                    3537                    12468                     2430 
Hst33_Nuclei_Multiome-v1 Hst36_Nuclei_Multiome-v1 Hst39_Nuclei_Multiome-v1 
                   32750                     6351                    23258 
Hst40_Nuclei_Multiome-v1 Hst41_Nuclei_Multiome-v1 
                    8705                    72887
```

Example 38 (unknown):
```unknown
___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 39 (unknown):
```unknown
class: ArchRProject 
outputDirectory: /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output 
samples(37): BHF_F_Hea11064670_BHF_F_Hea11031823
  BHF_F_Hea11064671_BHF_F_Hea11031824 ...
  HCAHeartST13386009_HCAHeartST13303419
  HCAHeartST13386010_HCAHeartST13303420
sampleColData names(1): ArrowFiles
cellColData names(55): Sample TSSEnrichment ... stress_score hb1_score
numberOfCells(1): 167022
medianTSS(1): 11.614
medianFrags(1): 10338.5
```

Example 40 (unknown):
```unknown
proj <- addClusters(
    input =proj,
    reducedDims = "Harmony",
    method = "Seurat",
    name = "Clusters",
    resolution = 0.8
)
```

Example 41 (unknown):
```unknown
ArchR logging to : ArchRLogs/ArchR-addClusters-1c3a682a96e4-Date-2023-03-09_Time-10-55-55.log
If there is an issue, please report to github with logFile!

2023-03-09 10:55:58 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0.007 mins elapsed.

Computing nearest neighbor graph

Computing SNN
```

Example 42 (unknown):
```unknown
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 167022
Number of edges: 5103432

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9367
Number of communities: 272
Elapsed time: 89 seconds
```

Example 43 (unknown):
```unknown
234 singletons identified. 38 final clusters.

2023-03-09 11:07:23 : Testing Biased Clusters, 11.426 mins elapsed.

2023-03-09 11:07:24 : Testing Outlier Clusters, 11.455 mins elapsed.

2023-03-09 11:07:25 : Assigning Outlier Clusters (n = 3, nOutlier < 5 cells) to Neighbors, 11.455 mins elapsed.

2023-03-09 11:07:25 : Identified more clusters than maxClusters allowed (n = 3). Merging clusters to maxClusters (n = 25).
If this is not desired set maxClusters = NULL!, 11.469 mins elapsed.

2023-03-09 11:07:26 : Assigning Cluster Names to 25 Clusters, 11.472 mins elapsed.

2023-03-09 11:07:26 : Finished addClusters, 11.477 mins elapsed.
```

Example 44 (unknown):
```unknown
head(proj$Clusters)
```

Example 45 (unknown):
```unknown
library(repr)

# Change plot size to 4 x 3
options(repr.plot.width=10, repr.plot.height=10)
```

Example 46 (unknown):
```unknown
cM <- confusionMatrix(paste0(proj$Clusters), paste0(proj$fine_grain))

library(pheatmap)
cM <- cM / Matrix::rowSums(cM)
p <- pheatmap::pheatmap(
    mat = as.matrix(cM), 
    color = paletteContinuous("whiteBlue"), 
    border_color = "black"
)
p
```

Example 47 (unknown):
```unknown
proj <- addUMAP(
    ArchRProj = proj, 
    reducedDims = "Harmony", 
    name = "UMAP", 
    nNeighbors = 30, 
    minDist = 0.5, 
    metric = "cosine"
)
```

Example 48 (python):
```python
11:07:26 UMAP embedding parameters a = 0.583 b = 1.334

11:07:27 Read 167022 rows and found 30 numeric columns

11:07:27 Using Annoy for neighbor search, n_neighbors = 30

11:07:27 Building Annoy index with metric = cosine, n_trees = 50

0%   10   20   30   40   50   60   70   80   90   100%

[----|----|----|----|----|----|----|----|----|----|

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*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
|

11:08:15 Writing NN index file to temp file /tmp/RtmpSjr0IA/file1c3a1d0b0164

11:08:16 Searching Annoy index using 13 threads, search_k = 3000

11:08:26 Annoy recall = 99.89%

11:08:29 Commencing smooth kNN distance calibration using 13 threads

11:08:39 Initializing from normalized Laplacian + noise

11:09:02 Commencing optimization for 200 epochs, with 8626560 positive edges

11:11:10 Optimization finished

11:11:10 Creating temp model dir /tmp/RtmpSjr0IA/dir1c3a4f664611

11:11:10 Creating dir /tmp/RtmpSjr0IA/dir1c3a4f664611

11:11:20 Changing to /tmp/RtmpSjr0IA/dir1c3a4f664611

11:11:20 Creating /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/Embeddings/Save-Uwot-UMAP-Params-Harmony-1c3a5c37709c-Date-2023-03-09_Time-11-11-10.tar
```

Example 49 (unknown):
```unknown
options(repr.plot.width=30, repr.plot.height=10)

p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "fine_grain", embedding = "UMAP")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "Clusters", embedding = "UMAP")
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "donor", embedding = "UMAP")
p4 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "week", embedding = "UMAP")
ggAlignPlots(p1,p2,p3,p4, type = "h")
```

Example 50 (unknown):
```unknown
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1c3aca214ca-Date-2023-03-09_Time-11-11-32.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 
Length of unique values greater than palette, interpolating..



ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1c3aca214ca-Date-2023-03-09_Time-11-11-32.log

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1c3a58bc8fe7-Date-2023-03-09_Time-11-11-34.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 
Length of unique values greater than palette, interpolating..



ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1c3a58bc8fe7-Date-2023-03-09_Time-11-11-34.log

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1c3a7fd8bf0b-Date-2023-03-09_Time-11-11-37.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1c3a7fd8bf0b-Date-2023-03-09_Time-11-11-37.log

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1c3a69343d9c-Date-2023-03-09_Time-11-11-39.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1c3a69343d9c-Date-2023-03-09_Time-11-11-39.log
```

Example 51 (unknown):
```unknown
plotPDF(p1,p2,p3,p4, name = "Global_Plot-UMAPs.pdf", ArchRProj = proj, addDOC = FALSE, width = 8, height = 8)
```

Example 52 (unknown):
```unknown
Plotting Ggplot!

Plotting Ggplot!

Plotting Ggplot!

Plotting Ggplot!
```

Example 53 (unknown):
```unknown
saveArchRProject(ArchRProj = proj, outputDirectory = "project_output", load = FALSE)
```

Example 54 (unknown):
```unknown
Copying Arrow Files...

Copying Arrow Files (1 of 37)

Copying Arrow Files (2 of 37)

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Copying Arrow Files (37 of 37)

Saving ArchRProject...
```

Example 55 (unknown):
```unknown
___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 56 (unknown):
```unknown
class: ArchRProject 
outputDirectory: /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output 
samples(37): BHF_F_Hea11064670_BHF_F_Hea11031823
  BHF_F_Hea11064671_BHF_F_Hea11031824 ...
  HCAHeartST13386009_HCAHeartST13303419
  HCAHeartST13386010_HCAHeartST13303420
sampleColData names(1): ArrowFiles
cellColData names(56): Sample TSSEnrichment ... hb1_score Clusters
numberOfCells(1): 167022
medianTSS(1): 11.614
medianFrags(1): 10338.5
```

Example 57 (unknown):
```unknown
filetxt<-file("foetal_ATAC_index.txt")
writeLines(proj$cellNames_mod, filetxt)
close(filetxt)
```

---

## Notebook

**URL:** http://127.0.0.1:9020/notebooks_html/Fig1_General_processing/ATAC/ATAC_preprocess/ArchR_no4_addGEX.html

**Contents:**
- Read in ArchR project¶
- AnnData to Seurat object¶
- Prepare RNA data¶
  - Prepare SingleCellExperiment¶
  - Add rowRanges data¶
  - Modify cellnames etc¶
- Add RNA data to ArchR object¶
- Save¶

What is rowRanges data? ref https://www.bioconductor.org/packages/devel/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html https://robertamezquita.github.io/orchestratingSingleCellAnalysis/data-infrastructure.html#the-essentials-of-sce

**Examples:**

Example 1 (unknown):
```unknown
library(ArchR)
library(tidyverse)
library(BSgenome.Hsapiens.UCSC.hg38)
library(SingleCellExperiment)
library(anndata)
# library(sceasy)
# library(reticulate)
# use_condaenv('cellpymc')
# loompy <- reticulate::import('loompy')
```

Example 2 (python):
```python
/ |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    

ArchR : Version 1.0.2
For more information see our website : www.ArchRProject.com
If you encounter a bug please report : https://github.com/GreenleafLab/ArchR/issues

Loading Required Packages...

	Loading Package : grid v4.0.4

	Loading Package : gridExtra v2.3

	Loading Package : gtools v3.9.3

	Loading Package : gtable v0.3.0

	Loading Package : ggplot2 v3.4.0

	Loading Package : magrittr v2.0.3

	Loading Package : plyr v1.8.8

	Loading Package : stringr v1.4.0

	Loading Package : data.table v1.14.4

	Loading Package : matrixStats v0.62.0

	Loading Package : S4Vectors v0.28.1

	Loading Package : GenomicRanges v1.42.0

	Loading Package : BiocGenerics v0.36.1

	Loading Package : Matrix v1.3.2

	Loading Package : Rcpp v1.0.9

	Loading Package : SummarizedExperiment v1.20.0

	Loading Package : rhdf5 v2.34.0

Warning message in system("timedatectl", intern = TRUE):
“running command 'timedatectl' had status 1”
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ tibble  3.1.8      ✔ purrr   0.3.4 
✔ tidyr   1.2.1      ✔ dplyr   1.0.10
✔ readr   2.1.3      ✔ forcats 0.5.1 
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::arrange()         masks plyr::arrange()
✖ dplyr::between()         masks data.table::between()
✖ dplyr::collapse()        masks IRanges::collapse()
✖ dplyr::combine()         masks Biobase::combine(), BiocGenerics::combine(), gridExtra::combine()
✖ purrr::compact()         masks plyr::compact()
✖ dplyr::count()           masks matrixStats::count(), plyr::count()
✖ dplyr::desc()            masks IRanges::desc(), plyr::desc()
✖ tidyr::expand()          masks Matrix::expand(), S4Vectors::expand()
✖ tidyr::extract()         masks magrittr::extract()
✖ dplyr::failwith()        masks plyr::failwith()
✖ dplyr::filter()          masks stats::filter()
✖ dplyr::first()           masks S4Vectors::first(), data.table::first()
✖ dplyr::id()              masks plyr::id()
✖ dplyr::lag()             masks stats::lag()
✖ dplyr::last()            masks data.table::last()
✖ dplyr::mutate()          masks plyr::mutate()
✖ tidyr::pack()            masks Matrix::pack()
✖ BiocGenerics::Position() masks ggplot2::Position(), base::Position()
✖ purrr::reduce()          masks GenomicRanges::reduce(), IRanges::reduce()
✖ dplyr::rename()          masks S4Vectors::rename(), plyr::rename()
✖ purrr::set_names()       masks magrittr::set_names()
✖ dplyr::slice()           masks IRanges::slice()
✖ dplyr::summarise()       masks plyr::summarise()
✖ dplyr::summarize()       masks plyr::summarize()
✖ purrr::transpose()       masks data.table::transpose()
✖ tidyr::unpack()          masks Matrix::unpack()
Loading required package: BSgenome

Loading required package: Biostrings

Loading required package: XVector


Attaching package: ‘XVector’


The following object is masked from ‘package:purrr’:

    compact


The following object is masked from ‘package:plyr’:

    compact



Attaching package: ‘Biostrings’


The following object is masked from ‘package:base’:

    strsplit


Loading required package: rtracklayer


Attaching package: ‘anndata’


The following object is masked from ‘package:readr’:

    read_csv
```

Example 3 (unknown):
```unknown
# before starting a project we must set the ArchRGenome and default threads for parallelization.
# Setting default genome to Hg38.
addArchRGenome("hg38")
```

Example 4 (unknown):
```unknown
Setting default genome to Hg38.
```

Example 5 (unknown):
```unknown
# Setting default number of Parallel threads to 16
addArchRThreads(threads = 1)
```

Example 6 (unknown):
```unknown
Setting default number of Parallel threads to 1.
```

Example 7 (unknown):
```unknown
archr_project_path = '/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output'
proj = loadArchRProject(path = archr_project_path, showLogo = FALSE)
proj
```

Example 8 (unknown):
```unknown
Successfully loaded ArchRProject!


           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 9 (unknown):
```unknown
class: ArchRProject 
outputDirectory: /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output 
samples(37): BHF_F_Hea11064670_BHF_F_Hea11031823
  BHF_F_Hea11064671_BHF_F_Hea11031824 ...
  HCAHeartST13386009_HCAHeartST13303419
  HCAHeartST13386010_HCAHeartST13303420
sampleColData names(1): ArrowFiles
cellColData names(59): Sample TSSEnrichment ... ReadsInPeaks FRIP
numberOfCells(1): 167022
medianTSS(1): 11.614
medianFrags(1): 10338.5
```

Example 10 (unknown):
```unknown
# convert anndata to seurat object
if(0){
    sceasy::convertFormat('/nfs/team205/heart/anndata_objects/Foetal/Feb28ObjectRaw_Multiome.h5ad', 
                      from="anndata", to="seurat",
                       outFile='/nfs/team205/heart/anndata_objects/Foetal/Feb28ObjectRaw_Multiome.rds')
}
```

Example 11 (unknown):
```unknown
X -> counts
```

Example 12 (python):
```python
An object of class Seurat 
36601 features across 211145 samples within 1 assay 
Active assay: RNA (36601 features, 0 variable features)
```

Example 13 (unknown):
```unknown
# read in seurat object
rna = readRDS('/nfs/team205/heart/anndata_objects/Foetal/Feb28ObjectRaw_Multiome.rds')
rna
```

Example 14 (python):
```python
Loading required package: SeuratObject


Attaching package: ‘SeuratObject’


The following object is masked from ‘package:SummarizedExperiment’:

    Assays
```

Example 15 (python):
```python
An object of class Seurat 
36601 features across 211145 samples within 1 assay 
Active assay: RNA (36601 features, 0 variable features)
```

Example 16 (unknown):
```unknown
# read in CellRanger h5 data for rowRanges data
rna_forRowRanges <- import10xFeatureMatrix(
    input = c("/nfs/team205/heart/mapped/cellranger-arc200/BHF_F_Hea13168898_BHF_F_Hea13168514/filtered_feature_bc_matrix.h5"),
    names = c("BHF_F_Hea13168898_BHF_F_Hea13168514")
   )
```

Example 17 (unknown):
```unknown
Importing Feature Matrix 1 of 1

Re-ordering RNA matricies for consistency.
```

Example 18 (unknown):
```unknown
# shared genes
shared_genes = intersect(rownames(rna_forRowRanges),rownames(rna))

# subset shared genes
rna = rna[shared_genes,]
rna_forRowRanges = rna_forRowRanges[shared_genes,]

# convert to SingleCellExperiment
rna = Seurat::as.SingleCellExperiment(rna)
rna
```

Example 19 (python):
```python
class: SingleCellExperiment 
dim: 36578 211145 
metadata(0):
assays(2): counts logcounts
rownames(36578): MIR1302-2HG FAM138A ... AC007325.4 AC007325.2
rowData names(1): gene_id
colnames(211145):
  BHF_F_Hea11064670_BHF_F_Hea11031823_TTGCTTAGTGAGACTC-1
  BHF_F_Hea11064670_BHF_F_Hea11031823_ATAGATGCATTGTCCT-1 ...
  HCAHeartST13386010_HCAHeartST13303420_CGTAATGGTATTGAGT-1
  HCAHeartST13386010_HCAHeartST13303420_GCTGTAAGTCAATACG-1
colData names(50): sangerID combinedID ... nFeature_RNA ident
reducedDimNames(0):
altExpNames(0):
```

Example 20 (unknown):
```unknown
rowRanges(rna_forRowRanges)
```

Example 21 (python):
```python
GRanges object with 36578 ranges and 5 metadata columns:
                seqnames          ranges strand |    feature_type genome
                   <Rle>       <IRanges>  <Rle> |           <Rle>  <Rle>
  MIR1302-2HG       chr1     29553-30267      * | Gene Expression GRCh38
      FAM138A       chr1     36080-36081      * | Gene Expression GRCh38
        OR4F5       chr1     65418-69055      * | Gene Expression GRCh38
   AL627309.3       chr1     91104-91105      * | Gene Expression GRCh38
   AL627309.1       chr1   120931-133723      * | Gene Expression GRCh38
          ...        ...             ...    ... .             ...    ...
   AC141272.1 KI270728.1 1270983-1270984      * | Gene Expression GRCh38
   AC023491.2 KI270731.1     13000-13001      * | Gene Expression GRCh38
   AC007325.1 KI270734.1     72410-72411      * | Gene Expression GRCh38
   AC007325.4 KI270734.1   131493-131494      * | Gene Expression GRCh38
   AC007325.2 KI270734.1   161749-161852      * | Gene Expression GRCh38
                           id               interval        name
                      <array>                <array>     <array>
  MIR1302-2HG ENSG00000243485       chr1:29553-30267 MIR1302-2HG
      FAM138A ENSG00000237613       chr1:36080-36081     FAM138A
        OR4F5 ENSG00000186092       chr1:65418-69055       OR4F5
   AL627309.3 ENSG00000239945       chr1:91104-91105  AL627309.3
   AL627309.1 ENSG00000238009     chr1:120931-133723  AL627309.1
          ...             ...                    ...         ...
   AC141272.1 ENSG00000277836 KI270728.1:1270983-1..  AC141272.1
   AC023491.2 ENSG00000278633 KI270731.1:13000-13001  AC023491.2
   AC007325.1 ENSG00000276017 KI270734.1:72410-72411  AC007325.1
   AC007325.4 ENSG00000278817 KI270734.1:131493-13..  AC007325.4
   AC007325.2 ENSG00000277196 KI270734.1:161749-16..  AC007325.2
  -------
  seqinfo: 39 sequences from an unspecified genome; no seqlengths
```

Example 22 (unknown):
```unknown
# add rowRanges data
rowRanges(rna) <- rowRanges(rna_forRowRanges)
```

Example 23 (javascript):
```javascript
# add barcode column
colData(rna)$cellbarcode = strsplit(colnames(rna), split = paste0(colData(rna)$combinedID,"_")) %>% lapply(function(x){x[2]}) %>% unlist()

# rename cell names to be matched with ArchR object
colnames(rna) = paste0(colData(rna)$combinedID,'#',colData(rna)$cellbarcode)
colnames(rna)[1:10]
```

Example 24 (unknown):
```unknown
# remove logcounts
assays(rna)['logcounts'] = NULL
rna
```

Example 25 (python):
```python
class: SingleCellExperiment 
dim: 36578 211145 
metadata(0):
assays(1): counts
rownames(36578): MIR1302-2HG FAM138A ... AC007325.4 AC007325.2
rowData names(5): feature_type genome id interval name
colnames(211145):
  BHF_F_Hea11064670_BHF_F_Hea11031823#TTGCTTAGTGAGACTC-1
  BHF_F_Hea11064670_BHF_F_Hea11031823#ATAGATGCATTGTCCT-1 ...
  HCAHeartST13386010_HCAHeartST13303420#CGTAATGGTATTGAGT-1
  HCAHeartST13386010_HCAHeartST13303420#GCTGTAAGTCAATACG-1
colData names(51): sangerID combinedID ... ident cellbarcode
reducedDimNames(0):
altExpNames(0):
```

Example 26 (unknown):
```unknown
head(proj$cellNames)
```

Example 27 (unknown):
```unknown
length(intersect(proj$cellNames,colnames(rna)))
```

Example 28 (unknown):
```unknown
# subset shared cells
# shared_cells = intersect(proj$cellNames,colnames(rna))
# proj_shared = proj[shared_cells, ]
```

Example 29 (unknown):
```unknown
proj <- addGeneExpressionMatrix(input = proj, seRNA = rna, force = TRUE)
proj
```

Example 30 (unknown):
```unknown
ArchR logging to : ArchRLogs/ArchR-addGeneExpressionMatrix-49213027a1f7-Date-2023-03-09_Time-22-44-06.log
If there is an issue, please report to github with logFile!

Overlap w/ scATAC = 1

2023-03-09 22:44:10 : 

Overlap Per Sample w/ scATAC : 7089STDY13216920_BHF_F_Hea13242527=10630,7089STDY13216921_BHF_F_Hea13242528=9214,7089STDY13216922_BHF_F_Hea13242529=3958,7089STDY13216923_BHF_F_Hea13242530=1,7089STDY13216924_BHF_F_Hea13242531=3783,7089STDY13216925_BHF_F_Hea13242532=2197,7089STDY13216926_BHF_F_Hea13242533=3622,7089STDY13216927_BHF_F_Hea13242534=4909,BHF_F_Hea11064670_BHF_F_Hea11031823=350,BHF_F_Hea11064671_BHF_F_Hea11031824=2218,BHF_F_Hea11064672_BHF_F_Hea11031825=3537,BHF_F_Hea11933666_BHF_F_Hea11596619=7905,BHF_F_Hea11933667_BHF_F_Hea11596620=8692,BHF_F_Hea11933668_BHF_F_Hea11596621=8194,BHF_F_Hea11933669_BHF_F_Hea11596622=7959,BHF_F_Hea11933670_BHF_F_Hea11596623=2824,BHF_F_Hea11933671_BHF_F_Hea11596624=3092,BHF_F_Hea11933672_BHF_F_Hea11596625=3143,BHF_F_Hea11933673_BHF_F_Hea11596626=3409,BHF_F_Hea11933674_BHF_F_Hea11596627=2239,BHF_F_Hea11933675_BHF_F_Hea11596628=191,BHF_F_Hea13168892_BHF_F_Hea13168508=3736,BHF_F_Hea13168893_BHF_F_Hea13168509=4405,BHF_F_Hea13168894_BHF_F_Hea13168510=5944,BHF_F_Hea13168895_BHF_F_Hea13168511=5525,BHF_F_Hea13168896_BHF_F_Hea13168512=8097,BHF_F_Hea13168897_BHF_F_Hea13168513=6693,BHF_F_Hea13168898_BHF_F_Hea13168514=8593,BHF_F_Hea13168899_BHF_F_Hea13168515=7575,BHF_F_Hea13188317_BHF_F_Hea13187619=2831,BHF_F_Hea13188318_BHF_F_Hea13187620=5195,BHF_F_Hea13188324_BHF_F_Hea13187626=5123,BHF_F_Hea13188328_BHF_F_Hea13187630=817,BHF_F_Hea13188329_BHF_F_Hea13187631=691,BHF_F_Hea13188330_BHF_F_Hea13187632=560,HCAHeartST13386009_HCAHeartST13303419=3882,HCAHeartST13386010_HCAHeartST13303420=5288

2023-03-09 22:44:11 : 

2023-03-09 22:44:52 : Batch Execution w/ safelapply!, 0 mins elapsed.

2023-03-09 22:44:55 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (1 of 23)!, 0.047 mins elapsed.

2023-03-09 22:44:59 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (2 of 23)!, 0.117 mins elapsed.

2023-03-09 22:45:02 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (3 of 23)!, 0.172 mins elapsed.

2023-03-09 22:45:07 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (4 of 23)!, 0.262 mins elapsed.

2023-03-09 22:45:11 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (5 of 23)!, 0.314 mins elapsed.

2023-03-09 22:45:14 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (6 of 23)!, 0.365 mins elapsed.

2023-03-09 22:45:18 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (7 of 23)!, 0.439 mins elapsed.

2023-03-09 22:45:22 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (8 of 23)!, 0.502 mins elapsed.

2023-03-09 22:45:26 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (9 of 23)!, 0.564 mins elapsed.

2023-03-09 22:45:30 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (10 of 23)!, 0.638 mins elapsed.

2023-03-09 22:45:33 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (11 of 23)!, 0.695 mins elapsed.

2023-03-09 22:45:37 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (12 of 23)!, 0.748 mins elapsed.

2023-03-09 22:45:41 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (13 of 23)!, 0.83 mins elapsed.

2023-03-09 22:45:45 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (14 of 23)!, 0.882 mins elapsed.

2023-03-09 22:45:48 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (15 of 23)!, 0.938 mins elapsed.

2023-03-09 22:45:53 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (16 of 23)!, 1.026 mins elapsed.

2023-03-09 22:45:57 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (17 of 23)!, 1.081 mins elapsed.

2023-03-09 22:46:00 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (18 of 23)!, 1.137 mins elapsed.

2023-03-09 22:46:05 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (19 of 23)!, 1.223 mins elapsed.

2023-03-09 22:46:08 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (20 of 23)!, 1.275 mins elapsed.

2023-03-09 22:46:11 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (21 of 23)!, 1.325 mins elapsed.

2023-03-09 22:46:15 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (22 of 23)!, 1.391 mins elapsed.

2023-03-09 22:46:18 : Adding 7089STDY13216921_BHF_F_Hea13242528 to GeneExpressionMatrix for Chr (23 of 23)!, 1.441 mins elapsed.

2023-03-09 22:46:25 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (1 of 23)!, 1.562 mins elapsed.

2023-03-09 22:46:29 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (2 of 23)!, 1.623 mins elapsed.

2023-03-09 22:46:33 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (3 of 23)!, 1.683 mins elapsed.

2023-03-09 22:46:37 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (4 of 23)!, 1.761 mins elapsed.

2023-03-09 22:46:41 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (5 of 23)!, 1.815 mins elapsed.

2023-03-09 22:46:44 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (6 of 23)!, 1.868 mins elapsed.

2023-03-09 22:46:48 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (7 of 23)!, 1.941 mins elapsed.

2023-03-09 22:46:52 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (8 of 23)!, 2.004 mins elapsed.

2023-03-09 22:46:55 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (9 of 23)!, 2.058 mins elapsed.

2023-03-09 22:47:00 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (10 of 23)!, 2.131 mins elapsed.

2023-03-09 22:47:03 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (11 of 23)!, 2.183 mins elapsed.

2023-03-09 22:47:06 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (12 of 23)!, 2.236 mins elapsed.

2023-03-09 22:47:10 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (13 of 23)!, 2.31 mins elapsed.

2023-03-09 22:47:13 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (14 of 23)!, 2.36 mins elapsed.

2023-03-09 22:47:17 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (15 of 23)!, 2.419 mins elapsed.

2023-03-09 22:47:22 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (16 of 23)!, 2.5 mins elapsed.

2023-03-09 22:47:25 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (17 of 23)!, 2.555 mins elapsed.

2023-03-09 22:47:28 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (18 of 23)!, 2.609 mins elapsed.

2023-03-09 22:47:32 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (19 of 23)!, 2.678 mins elapsed.

2023-03-09 22:47:35 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (20 of 23)!, 2.73 mins elapsed.

2023-03-09 22:47:39 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (21 of 23)!, 2.785 mins elapsed.

2023-03-09 22:47:44 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (22 of 23)!, 2.87 mins elapsed.

2023-03-09 22:47:47 : Adding 7089STDY13216920_BHF_F_Hea13242527 to GeneExpressionMatrix for Chr (23 of 23)!, 2.93 mins elapsed.

2023-03-09 22:47:55 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (1 of 23)!, 3.05 mins elapsed.

2023-03-09 22:47:58 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (2 of 23)!, 3.103 mins elapsed.

2023-03-09 22:48:01 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (3 of 23)!, 3.155 mins elapsed.

2023-03-09 22:48:05 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (4 of 23)!, 3.228 mins elapsed.

2023-03-09 22:48:08 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (5 of 23)!, 3.278 mins elapsed.

2023-03-09 22:48:11 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (6 of 23)!, 3.33 mins elapsed.

2023-03-09 22:48:16 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (7 of 23)!, 3.398 mins elapsed.

2023-03-09 22:48:19 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (8 of 23)!, 3.448 mins elapsed.

2023-03-09 22:48:21 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (9 of 23)!, 3.497 mins elapsed.

2023-03-09 22:48:26 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (10 of 23)!, 3.566 mins elapsed.

2023-03-09 22:48:29 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (11 of 23)!, 3.616 mins elapsed.

2023-03-09 22:48:32 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (12 of 23)!, 3.666 mins elapsed.

2023-03-09 22:48:36 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (13 of 23)!, 3.734 mins elapsed.

2023-03-09 22:48:39 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (14 of 23)!, 3.794 mins elapsed.

2023-03-09 22:48:42 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (15 of 23)!, 3.844 mins elapsed.

2023-03-09 22:48:46 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (16 of 23)!, 3.912 mins elapsed.

2023-03-09 22:48:49 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (17 of 23)!, 3.961 mins elapsed.

2023-03-09 22:48:52 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (18 of 23)!, 4.009 mins elapsed.

2023-03-09 22:48:56 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (19 of 23)!, 4.075 mins elapsed.

2023-03-09 22:48:59 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (20 of 23)!, 4.129 mins elapsed.

2023-03-09 22:49:02 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (21 of 23)!, 4.177 mins elapsed.

2023-03-09 22:49:06 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (22 of 23)!, 4.243 mins elapsed.

2023-03-09 22:49:09 : Adding BHF_F_Hea13188318_BHF_F_Hea13187620 to GeneExpressionMatrix for Chr (23 of 23)!, 4.289 mins elapsed.

2023-03-09 22:49:16 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (1 of 23)!, 4.405 mins elapsed.

2023-03-09 22:49:19 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (2 of 23)!, 4.459 mins elapsed.

2023-03-09 22:49:22 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (3 of 23)!, 4.51 mins elapsed.

2023-03-09 22:49:27 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (4 of 23)!, 4.592 mins elapsed.

2023-03-09 22:49:30 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (5 of 23)!, 4.645 mins elapsed.

2023-03-09 22:49:33 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (6 of 23)!, 4.695 mins elapsed.

2023-03-09 22:49:38 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (7 of 23)!, 4.779 mins elapsed.

2023-03-09 22:49:42 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (8 of 23)!, 4.831 mins elapsed.

2023-03-09 22:49:44 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (9 of 23)!, 4.879 mins elapsed.

2023-03-09 22:49:49 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (10 of 23)!, 4.952 mins elapsed.

2023-03-09 22:49:52 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (11 of 23)!, 5.001 mins elapsed.

2023-03-09 22:49:55 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (12 of 23)!, 5.052 mins elapsed.

2023-03-09 22:49:59 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (13 of 23)!, 5.123 mins elapsed.

2023-03-09 22:50:02 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (14 of 23)!, 5.173 mins elapsed.

2023-03-09 22:50:05 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (15 of 23)!, 5.222 mins elapsed.

2023-03-09 22:50:09 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (16 of 23)!, 5.29 mins elapsed.

2023-03-09 22:50:12 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (17 of 23)!, 5.338 mins elapsed.

2023-03-09 22:50:15 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (18 of 23)!, 5.387 mins elapsed.

2023-03-09 22:50:19 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (19 of 23)!, 5.453 mins elapsed.

2023-03-09 22:50:22 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (20 of 23)!, 5.502 mins elapsed.

2023-03-09 22:50:25 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (21 of 23)!, 5.55 mins elapsed.

2023-03-09 22:50:29 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (22 of 23)!, 5.617 mins elapsed.

2023-03-09 22:50:32 : Adding 7089STDY13216924_BHF_F_Hea13242531 to GeneExpressionMatrix for Chr (23 of 23)!, 5.664 mins elapsed.

2023-03-09 22:50:41 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (1 of 23)!, 5.819 mins elapsed.

2023-03-09 22:50:44 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (2 of 23)!, 5.877 mins elapsed.

2023-03-09 22:50:48 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (3 of 23)!, 5.933 mins elapsed.

2023-03-09 22:50:52 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (4 of 23)!, 6.008 mins elapsed.

2023-03-09 22:50:55 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (5 of 23)!, 6.059 mins elapsed.

2023-03-09 22:50:58 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (6 of 23)!, 6.112 mins elapsed.

2023-03-09 22:51:03 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (7 of 23)!, 6.187 mins elapsed.

2023-03-09 22:51:06 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (8 of 23)!, 6.241 mins elapsed.

2023-03-09 22:51:10 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (9 of 23)!, 6.298 mins elapsed.

2023-03-09 22:51:14 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (10 of 23)!, 6.368 mins elapsed.

2023-03-09 22:51:17 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (11 of 23)!, 6.42 mins elapsed.

2023-03-09 22:51:20 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (12 of 23)!, 6.473 mins elapsed.

2023-03-09 22:51:24 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (13 of 23)!, 6.546 mins elapsed.

2023-03-09 22:51:27 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (14 of 23)!, 6.597 mins elapsed.

2023-03-09 22:51:31 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (15 of 23)!, 6.647 mins elapsed.

2023-03-09 22:51:35 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (16 of 23)!, 6.718 mins elapsed.

2023-03-09 22:51:38 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (17 of 23)!, 6.769 mins elapsed.

2023-03-09 22:51:41 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (18 of 23)!, 6.822 mins elapsed.

2023-03-09 22:51:45 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (19 of 23)!, 6.891 mins elapsed.

2023-03-09 22:51:48 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (20 of 23)!, 6.945 mins elapsed.

2023-03-09 22:51:51 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (21 of 23)!, 6.996 mins elapsed.

2023-03-09 22:51:56 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (22 of 23)!, 7.064 mins elapsed.

2023-03-09 22:51:58 : Adding BHF_F_Hea11933667_BHF_F_Hea11596620 to GeneExpressionMatrix for Chr (23 of 23)!, 7.113 mins elapsed.

2023-03-09 22:52:05 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (1 of 23)!, 7.227 mins elapsed.

2023-03-09 22:52:08 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (2 of 23)!, 7.279 mins elapsed.

2023-03-09 22:52:12 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (3 of 23)!, 7.335 mins elapsed.

2023-03-09 22:52:16 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (4 of 23)!, 7.405 mins elapsed.

2023-03-09 22:52:19 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (5 of 23)!, 7.454 mins elapsed.

2023-03-09 22:52:22 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (6 of 23)!, 7.507 mins elapsed.

2023-03-09 22:52:26 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (7 of 23)!, 7.576 mins elapsed.

2023-03-09 22:52:29 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (8 of 23)!, 7.625 mins elapsed.

2023-03-09 22:52:32 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (9 of 23)!, 7.674 mins elapsed.

2023-03-09 22:52:36 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (10 of 23)!, 7.742 mins elapsed.

2023-03-09 22:52:39 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (11 of 23)!, 7.791 mins elapsed.

2023-03-09 22:52:42 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (12 of 23)!, 7.841 mins elapsed.

2023-03-09 22:52:46 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (13 of 23)!, 7.91 mins elapsed.

2023-03-09 22:52:49 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (14 of 23)!, 7.958 mins elapsed.

2023-03-09 22:52:52 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (15 of 23)!, 8.006 mins elapsed.

2023-03-09 22:52:56 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (16 of 23)!, 8.073 mins elapsed.

2023-03-09 22:52:59 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (17 of 23)!, 8.124 mins elapsed.

2023-03-09 22:53:02 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (18 of 23)!, 8.174 mins elapsed.

2023-03-09 22:53:06 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (19 of 23)!, 8.242 mins elapsed.

2023-03-09 22:53:10 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (20 of 23)!, 8.304 mins elapsed.

2023-03-09 22:53:13 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (21 of 23)!, 8.358 mins elapsed.

2023-03-09 22:53:17 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (22 of 23)!, 8.425 mins elapsed.

2023-03-09 22:53:20 : Adding HCAHeartST13386010_HCAHeartST13303420 to GeneExpressionMatrix for Chr (23 of 23)!, 8.475 mins elapsed.

2023-03-09 22:53:27 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (1 of 23)!, 8.582 mins elapsed.

2023-03-09 22:53:29 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (2 of 23)!, 8.63 mins elapsed.

2023-03-09 22:53:32 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (3 of 23)!, 8.677 mins elapsed.

2023-03-09 22:53:36 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (4 of 23)!, 8.744 mins elapsed.

2023-03-09 22:53:39 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (5 of 23)!, 8.791 mins elapsed.

2023-03-09 22:53:42 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (6 of 23)!, 8.838 mins elapsed.

2023-03-09 22:53:46 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (7 of 23)!, 8.904 mins elapsed.

2023-03-09 22:53:49 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (8 of 23)!, 8.951 mins elapsed.

2023-03-09 22:53:51 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (9 of 23)!, 8.996 mins elapsed.

2023-03-09 22:53:55 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (10 of 23)!, 9.062 mins elapsed.

2023-03-09 22:53:58 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (11 of 23)!, 9.108 mins elapsed.

2023-03-09 22:54:01 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (12 of 23)!, 9.154 mins elapsed.

2023-03-09 22:54:05 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (13 of 23)!, 9.223 mins elapsed.

2023-03-09 22:54:08 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (14 of 23)!, 9.268 mins elapsed.

2023-03-09 22:54:10 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (15 of 23)!, 9.313 mins elapsed.

2023-03-09 22:54:14 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (16 of 23)!, 9.377 mins elapsed.

2023-03-09 22:54:17 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (17 of 23)!, 9.422 mins elapsed.

2023-03-09 22:54:20 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (18 of 23)!, 9.468 mins elapsed.

2023-03-09 22:54:24 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (19 of 23)!, 9.532 mins elapsed.

2023-03-09 22:54:26 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (20 of 23)!, 9.577 mins elapsed.

2023-03-09 22:54:29 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (21 of 23)!, 9.624 mins elapsed.

2023-03-09 22:54:33 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (22 of 23)!, 9.689 mins elapsed.

2023-03-09 22:54:36 : Adding 7089STDY13216925_BHF_F_Hea13242532 to GeneExpressionMatrix for Chr (23 of 23)!, 9.734 mins elapsed.

2023-03-09 22:54:43 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (1 of 23)!, 9.849 mins elapsed.

2023-03-09 22:54:46 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (2 of 23)!, 9.906 mins elapsed.

2023-03-09 22:54:49 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (3 of 23)!, 9.961 mins elapsed.

2023-03-09 22:54:54 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (4 of 23)!, 10.034 mins elapsed.

2023-03-09 22:54:57 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (5 of 23)!, 10.086 mins elapsed.

2023-03-09 22:55:00 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (6 of 23)!, 10.138 mins elapsed.

2023-03-09 22:55:05 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (7 of 23)!, 10.226 mins elapsed.

2023-03-09 22:55:08 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (8 of 23)!, 10.279 mins elapsed.

2023-03-09 22:55:11 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (9 of 23)!, 10.329 mins elapsed.

2023-03-09 22:55:16 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (10 of 23)!, 10.402 mins elapsed.

2023-03-09 22:55:19 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (11 of 23)!, 10.455 mins elapsed.

2023-03-09 22:55:22 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (12 of 23)!, 10.508 mins elapsed.

2023-03-09 22:55:26 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (13 of 23)!, 10.58 mins elapsed.

2023-03-09 22:55:29 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (14 of 23)!, 10.629 mins elapsed.

2023-03-09 22:55:32 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (15 of 23)!, 10.679 mins elapsed.

2023-03-09 22:55:36 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (16 of 23)!, 10.746 mins elapsed.

2023-03-09 22:55:39 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (17 of 23)!, 10.795 mins elapsed.

2023-03-09 22:55:42 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (18 of 23)!, 10.846 mins elapsed.

2023-03-09 22:55:46 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (19 of 23)!, 10.912 mins elapsed.

2023-03-09 22:55:49 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (20 of 23)!, 10.962 mins elapsed.

2023-03-09 22:55:52 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (21 of 23)!, 11.011 mins elapsed.

2023-03-09 22:55:56 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (22 of 23)!, 11.078 mins elapsed.

2023-03-09 22:55:59 : Adding BHF_F_Hea11933666_BHF_F_Hea11596619 to GeneExpressionMatrix for Chr (23 of 23)!, 11.126 mins elapsed.

2023-03-09 22:56:06 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (1 of 23)!, 11.236 mins elapsed.

2023-03-09 22:56:09 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (2 of 23)!, 11.294 mins elapsed.

2023-03-09 22:56:13 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (3 of 23)!, 11.347 mins elapsed.

2023-03-09 22:56:17 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (4 of 23)!, 11.416 mins elapsed.

2023-03-09 22:56:20 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (5 of 23)!, 11.464 mins elapsed.

2023-03-09 22:56:23 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (6 of 23)!, 11.514 mins elapsed.

2023-03-09 22:56:27 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (7 of 23)!, 11.584 mins elapsed.

2023-03-09 22:56:30 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (8 of 23)!, 11.644 mins elapsed.

2023-03-09 22:56:34 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (9 of 23)!, 11.704 mins elapsed.

2023-03-09 22:56:38 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (10 of 23)!, 11.776 mins elapsed.

2023-03-09 22:56:41 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (11 of 23)!, 11.828 mins elapsed.

2023-03-09 22:56:45 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (12 of 23)!, 11.89 mins elapsed.

2023-03-09 22:56:50 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (13 of 23)!, 11.972 mins elapsed.

2023-03-09 22:56:53 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (14 of 23)!, 12.024 mins elapsed.

2023-03-09 22:56:56 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (15 of 23)!, 12.074 mins elapsed.

2023-03-09 22:57:00 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (16 of 23)!, 12.144 mins elapsed.

2023-03-09 22:57:03 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (17 of 23)!, 12.192 mins elapsed.

2023-03-09 22:57:06 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (18 of 23)!, 12.241 mins elapsed.

2023-03-09 22:57:10 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (19 of 23)!, 12.309 mins elapsed.

2023-03-09 22:57:13 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (20 of 23)!, 12.356 mins elapsed.

2023-03-09 22:57:16 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (21 of 23)!, 12.404 mins elapsed.

2023-03-09 22:57:20 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (22 of 23)!, 12.47 mins elapsed.

2023-03-09 22:57:23 : Adding BHF_F_Hea13188324_BHF_F_Hea13187626 to GeneExpressionMatrix for Chr (23 of 23)!, 12.525 mins elapsed.

2023-03-09 22:57:33 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (1 of 23)!, 12.689 mins elapsed.

2023-03-09 22:57:37 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (2 of 23)!, 12.753 mins elapsed.

2023-03-09 22:57:40 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (3 of 23)!, 12.811 mins elapsed.

2023-03-09 22:57:45 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (4 of 23)!, 12.882 mins elapsed.

2023-03-09 22:57:48 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (5 of 23)!, 12.935 mins elapsed.

2023-03-09 22:57:51 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (6 of 23)!, 12.988 mins elapsed.

2023-03-09 22:57:57 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (7 of 23)!, 13.081 mins elapsed.

2023-03-09 22:58:00 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (8 of 23)!, 13.143 mins elapsed.

2023-03-09 22:58:03 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (9 of 23)!, 13.195 mins elapsed.

2023-03-09 22:58:08 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (10 of 23)!, 13.276 mins elapsed.

2023-03-09 22:58:12 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (11 of 23)!, 13.335 mins elapsed.

2023-03-09 22:58:15 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (12 of 23)!, 13.389 mins elapsed.

2023-03-09 22:58:19 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (13 of 23)!, 13.462 mins elapsed.

2023-03-09 22:58:22 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (14 of 23)!, 13.511 mins elapsed.

2023-03-09 22:58:25 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (15 of 23)!, 13.562 mins elapsed.

2023-03-09 22:58:30 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (16 of 23)!, 13.64 mins elapsed.

2023-03-09 22:58:33 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (17 of 23)!, 13.691 mins elapsed.

2023-03-09 22:58:37 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (18 of 23)!, 13.756 mins elapsed.

2023-03-09 22:58:42 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (19 of 23)!, 13.843 mins elapsed.

2023-03-09 22:58:46 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (20 of 23)!, 13.909 mins elapsed.

2023-03-09 22:58:49 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (21 of 23)!, 13.96 mins elapsed.

2023-03-09 22:58:53 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (22 of 23)!, 14.029 mins elapsed.

2023-03-09 22:58:56 : Adding BHF_F_Hea11933668_BHF_F_Hea11596621 to GeneExpressionMatrix for Chr (23 of 23)!, 14.079 mins elapsed.

2023-03-09 22:59:03 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (1 of 23)!, 14.192 mins elapsed.

2023-03-09 22:59:07 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (2 of 23)!, 14.249 mins elapsed.

2023-03-09 22:59:10 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (3 of 23)!, 14.3 mins elapsed.

2023-03-09 22:59:14 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (4 of 23)!, 14.369 mins elapsed.

2023-03-09 22:59:17 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (5 of 23)!, 14.421 mins elapsed.

2023-03-09 22:59:21 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (6 of 23)!, 14.481 mins elapsed.

2023-03-09 22:59:25 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (7 of 23)!, 14.557 mins elapsed.

2023-03-09 22:59:28 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (8 of 23)!, 14.606 mins elapsed.

2023-03-09 22:59:31 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (9 of 23)!, 14.653 mins elapsed.

2023-03-09 22:59:35 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (10 of 23)!, 14.722 mins elapsed.

2023-03-09 22:59:38 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (11 of 23)!, 14.77 mins elapsed.

2023-03-09 22:59:41 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (12 of 23)!, 14.818 mins elapsed.

2023-03-09 22:59:45 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (13 of 23)!, 14.885 mins elapsed.

2023-03-09 22:59:48 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (14 of 23)!, 14.931 mins elapsed.

2023-03-09 22:59:50 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (15 of 23)!, 14.978 mins elapsed.

2023-03-09 22:59:54 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (16 of 23)!, 15.047 mins elapsed.

2023-03-09 22:59:57 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (17 of 23)!, 15.097 mins elapsed.

2023-03-09 23:00:00 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (18 of 23)!, 15.145 mins elapsed.

2023-03-09 23:00:05 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (19 of 23)!, 15.22 mins elapsed.

2023-03-09 23:00:08 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (20 of 23)!, 15.279 mins elapsed.

2023-03-09 23:00:11 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (21 of 23)!, 15.326 mins elapsed.

2023-03-09 23:00:16 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (22 of 23)!, 15.404 mins elapsed.

2023-03-09 23:00:19 : Adding HCAHeartST13386009_HCAHeartST13303419 to GeneExpressionMatrix for Chr (23 of 23)!, 15.45 mins elapsed.

2023-03-09 23:00:26 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (1 of 23)!, 15.567 mins elapsed.

2023-03-09 23:00:29 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (2 of 23)!, 15.625 mins elapsed.

2023-03-09 23:00:33 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (3 of 23)!, 15.692 mins elapsed.

2023-03-09 23:00:38 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (4 of 23)!, 15.765 mins elapsed.

2023-03-09 23:00:41 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (5 of 23)!, 15.815 mins elapsed.

2023-03-09 23:00:44 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (6 of 23)!, 15.866 mins elapsed.

2023-03-09 23:00:48 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (7 of 23)!, 15.938 mins elapsed.

2023-03-09 23:00:51 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (8 of 23)!, 15.99 mins elapsed.

2023-03-09 23:00:54 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (9 of 23)!, 16.04 mins elapsed.

2023-03-09 23:00:58 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (10 of 23)!, 16.109 mins elapsed.

2023-03-09 23:01:01 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (11 of 23)!, 16.16 mins elapsed.

2023-03-09 23:01:04 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (12 of 23)!, 16.213 mins elapsed.

2023-03-09 23:01:09 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (13 of 23)!, 16.283 mins elapsed.

2023-03-09 23:01:12 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (14 of 23)!, 16.338 mins elapsed.

2023-03-09 23:01:15 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (15 of 23)!, 16.392 mins elapsed.

2023-03-09 23:01:19 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (16 of 23)!, 16.462 mins elapsed.

2023-03-09 23:01:22 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (17 of 23)!, 16.513 mins elapsed.

2023-03-09 23:01:26 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (18 of 23)!, 16.565 mins elapsed.

2023-03-09 23:01:30 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (19 of 23)!, 16.634 mins elapsed.

2023-03-09 23:01:33 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (20 of 23)!, 16.686 mins elapsed.

2023-03-09 23:01:36 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (21 of 23)!, 16.746 mins elapsed.

2023-03-09 23:01:41 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (22 of 23)!, 16.815 mins elapsed.

2023-03-09 23:01:44 : Adding BHF_F_Hea11933669_BHF_F_Hea11596622 to GeneExpressionMatrix for Chr (23 of 23)!, 16.865 mins elapsed.

2023-03-09 23:01:51 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (1 of 23)!, 16.984 mins elapsed.

2023-03-09 23:01:54 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (2 of 23)!, 17.044 mins elapsed.

2023-03-09 23:01:58 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (3 of 23)!, 17.104 mins elapsed.

2023-03-09 23:02:03 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (4 of 23)!, 17.183 mins elapsed.

2023-03-09 23:02:06 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (5 of 23)!, 17.234 mins elapsed.

2023-03-09 23:02:09 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (6 of 23)!, 17.287 mins elapsed.

2023-03-09 23:02:13 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (7 of 23)!, 17.36 mins elapsed.

2023-03-09 23:02:16 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (8 of 23)!, 17.411 mins elapsed.

2023-03-09 23:02:19 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (9 of 23)!, 17.46 mins elapsed.

2023-03-09 23:02:23 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (10 of 23)!, 17.53 mins elapsed.

2023-03-09 23:02:27 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (11 of 23)!, 17.585 mins elapsed.

2023-03-09 23:02:30 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (12 of 23)!, 17.647 mins elapsed.

2023-03-09 23:02:35 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (13 of 23)!, 17.717 mins elapsed.

2023-03-09 23:02:38 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (14 of 23)!, 17.768 mins elapsed.

2023-03-09 23:02:41 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (15 of 23)!, 17.817 mins elapsed.

2023-03-09 23:02:45 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (16 of 23)!, 17.89 mins elapsed.

2023-03-09 23:02:48 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (17 of 23)!, 17.94 mins elapsed.

2023-03-09 23:02:51 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (18 of 23)!, 17.993 mins elapsed.

2023-03-09 23:02:55 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (19 of 23)!, 18.059 mins elapsed.

2023-03-09 23:02:58 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (20 of 23)!, 18.11 mins elapsed.

2023-03-09 23:03:02 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (21 of 23)!, 18.169 mins elapsed.

2023-03-09 23:03:07 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (22 of 23)!, 18.254 mins elapsed.

2023-03-09 23:03:10 : Adding BHF_F_Hea13168898_BHF_F_Hea13168514 to GeneExpressionMatrix for Chr (23 of 23)!, 18.303 mins elapsed.

2023-03-09 23:03:17 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (1 of 23)!, 18.42 mins elapsed.

2023-03-09 23:03:20 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (2 of 23)!, 18.479 mins elapsed.

2023-03-09 23:03:24 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (3 of 23)!, 18.533 mins elapsed.

2023-03-09 23:03:29 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (4 of 23)!, 18.618 mins elapsed.

2023-03-09 23:03:32 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (5 of 23)!, 18.669 mins elapsed.

2023-03-09 23:03:35 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (6 of 23)!, 18.721 mins elapsed.

2023-03-09 23:03:39 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (7 of 23)!, 18.792 mins elapsed.

2023-03-09 23:03:42 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (8 of 23)!, 18.843 mins elapsed.

2023-03-09 23:03:45 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (9 of 23)!, 18.892 mins elapsed.

2023-03-09 23:03:49 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (10 of 23)!, 18.961 mins elapsed.

2023-03-09 23:03:52 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (11 of 23)!, 19.011 mins elapsed.

2023-03-09 23:03:55 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (12 of 23)!, 19.062 mins elapsed.

2023-03-09 23:04:00 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (13 of 23)!, 19.133 mins elapsed.

2023-03-09 23:04:03 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (14 of 23)!, 19.181 mins elapsed.

2023-03-09 23:04:05 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (15 of 23)!, 19.229 mins elapsed.

2023-03-09 23:04:10 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (16 of 23)!, 19.298 mins elapsed.

2023-03-09 23:04:13 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (17 of 23)!, 19.348 mins elapsed.

2023-03-09 23:04:16 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (18 of 23)!, 19.397 mins elapsed.

2023-03-09 23:04:20 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (19 of 23)!, 19.465 mins elapsed.

2023-03-09 23:04:23 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (20 of 23)!, 19.515 mins elapsed.

2023-03-09 23:04:25 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (21 of 23)!, 19.563 mins elapsed.

2023-03-09 23:04:29 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (22 of 23)!, 19.629 mins elapsed.

2023-03-09 23:04:32 : Adding BHF_F_Hea13168896_BHF_F_Hea13168512 to GeneExpressionMatrix for Chr (23 of 23)!, 19.675 mins elapsed.

2023-03-09 23:04:39 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (1 of 23)!, 19.793 mins elapsed.

2023-03-09 23:04:43 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (2 of 23)!, 19.86 mins elapsed.

2023-03-09 23:04:46 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (3 of 23)!, 19.911 mins elapsed.

2023-03-09 23:04:50 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (4 of 23)!, 19.98 mins elapsed.

2023-03-09 23:04:53 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (5 of 23)!, 20.029 mins elapsed.

2023-03-09 23:04:56 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (6 of 23)!, 20.078 mins elapsed.

2023-03-09 23:05:01 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (7 of 23)!, 20.152 mins elapsed.

2023-03-09 23:05:04 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (8 of 23)!, 20.202 mins elapsed.

2023-03-09 23:05:07 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (9 of 23)!, 20.261 mins elapsed.

2023-03-09 23:05:13 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (10 of 23)!, 20.347 mins elapsed.

2023-03-09 23:05:16 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (11 of 23)!, 20.397 mins elapsed.

2023-03-09 23:05:19 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (12 of 23)!, 20.449 mins elapsed.

2023-03-09 23:05:23 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (13 of 23)!, 20.518 mins elapsed.

2023-03-09 23:05:26 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (14 of 23)!, 20.567 mins elapsed.

2023-03-09 23:05:29 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (15 of 23)!, 20.621 mins elapsed.

2023-03-09 23:05:33 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (16 of 23)!, 20.691 mins elapsed.

2023-03-09 23:05:36 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (17 of 23)!, 20.741 mins elapsed.

2023-03-09 23:05:40 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (18 of 23)!, 20.802 mins elapsed.

2023-03-09 23:05:44 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (19 of 23)!, 20.868 mins elapsed.

2023-03-09 23:05:47 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (20 of 23)!, 20.929 mins elapsed.

2023-03-09 23:05:50 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (21 of 23)!, 20.979 mins elapsed.

2023-03-09 23:05:55 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (22 of 23)!, 21.056 mins elapsed.

2023-03-09 23:05:58 : Adding BHF_F_Hea13168894_BHF_F_Hea13168510 to GeneExpressionMatrix for Chr (23 of 23)!, 21.103 mins elapsed.

2023-03-09 23:06:06 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (1 of 23)!, 21.246 mins elapsed.

2023-03-09 23:06:09 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (2 of 23)!, 21.296 mins elapsed.

2023-03-09 23:06:12 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (3 of 23)!, 21.344 mins elapsed.

2023-03-09 23:06:16 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (4 of 23)!, 21.412 mins elapsed.

2023-03-09 23:06:19 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (5 of 23)!, 21.46 mins elapsed.

2023-03-09 23:06:22 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (6 of 23)!, 21.51 mins elapsed.

2023-03-09 23:06:27 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (7 of 23)!, 21.582 mins elapsed.

2023-03-09 23:06:30 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (8 of 23)!, 21.631 mins elapsed.

2023-03-09 23:06:32 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (9 of 23)!, 21.678 mins elapsed.

2023-03-09 23:06:36 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (10 of 23)!, 21.745 mins elapsed.

2023-03-09 23:06:39 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (11 of 23)!, 21.795 mins elapsed.

2023-03-09 23:06:42 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (12 of 23)!, 21.844 mins elapsed.

2023-03-09 23:06:46 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (13 of 23)!, 21.912 mins elapsed.

2023-03-09 23:06:49 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (14 of 23)!, 21.96 mins elapsed.

2023-03-09 23:06:52 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (15 of 23)!, 22.008 mins elapsed.

2023-03-09 23:06:56 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (16 of 23)!, 22.076 mins elapsed.

2023-03-09 23:06:59 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (17 of 23)!, 22.13 mins elapsed.

2023-03-09 23:07:03 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (18 of 23)!, 22.185 mins elapsed.

2023-03-09 23:07:07 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (19 of 23)!, 22.25 mins elapsed.

2023-03-09 23:07:10 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (20 of 23)!, 22.298 mins elapsed.

2023-03-09 23:07:13 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (21 of 23)!, 22.347 mins elapsed.

2023-03-09 23:07:17 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (22 of 23)!, 22.42 mins elapsed.

2023-03-09 23:07:20 : Adding 7089STDY13216927_BHF_F_Hea13242534 to GeneExpressionMatrix for Chr (23 of 23)!, 22.466 mins elapsed.

2023-03-09 23:07:27 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (1 of 23)!, 22.584 mins elapsed.

2023-03-09 23:07:30 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (2 of 23)!, 22.638 mins elapsed.

2023-03-09 23:07:33 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (3 of 23)!, 22.688 mins elapsed.

2023-03-09 23:07:37 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (4 of 23)!, 22.759 mins elapsed.

2023-03-09 23:07:40 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (5 of 23)!, 22.812 mins elapsed.

2023-03-09 23:07:43 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (6 of 23)!, 22.863 mins elapsed.

2023-03-09 23:07:48 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (7 of 23)!, 22.933 mins elapsed.

2023-03-09 23:07:51 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (8 of 23)!, 22.983 mins elapsed.

2023-03-09 23:07:54 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (9 of 23)!, 23.031 mins elapsed.

2023-03-09 23:07:58 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (10 of 23)!, 23.1 mins elapsed.

2023-03-09 23:08:01 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (11 of 23)!, 23.162 mins elapsed.

2023-03-09 23:08:05 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (12 of 23)!, 23.224 mins elapsed.

2023-03-09 23:08:09 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (13 of 23)!, 23.296 mins elapsed.

2023-03-09 23:08:12 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (14 of 23)!, 23.344 mins elapsed.

2023-03-09 23:08:15 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (15 of 23)!, 23.394 mins elapsed.

2023-03-09 23:08:19 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (16 of 23)!, 23.463 mins elapsed.

2023-03-09 23:08:22 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (17 of 23)!, 23.512 mins elapsed.

2023-03-09 23:08:25 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (18 of 23)!, 23.561 mins elapsed.

2023-03-09 23:08:29 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (19 of 23)!, 23.629 mins elapsed.

2023-03-09 23:08:32 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (20 of 23)!, 23.679 mins elapsed.

2023-03-09 23:08:36 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (21 of 23)!, 23.731 mins elapsed.

2023-03-09 23:08:40 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (22 of 23)!, 23.799 mins elapsed.

2023-03-09 23:08:42 : Adding BHF_F_Hea13168895_BHF_F_Hea13168511 to GeneExpressionMatrix for Chr (23 of 23)!, 23.846 mins elapsed.

2023-03-09 23:08:49 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (1 of 23)!, 23.957 mins elapsed.

2023-03-09 23:08:52 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (2 of 23)!, 24.009 mins elapsed.

2023-03-09 23:08:55 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (3 of 23)!, 24.059 mins elapsed.

2023-03-09 23:08:59 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (4 of 23)!, 24.127 mins elapsed.

2023-03-09 23:09:02 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (5 of 23)!, 24.175 mins elapsed.

2023-03-09 23:09:05 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (6 of 23)!, 24.223 mins elapsed.

2023-03-09 23:09:09 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (7 of 23)!, 24.291 mins elapsed.

2023-03-09 23:09:12 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (8 of 23)!, 24.342 mins elapsed.

2023-03-09 23:09:15 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (9 of 23)!, 24.389 mins elapsed.

2023-03-09 23:09:19 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (10 of 23)!, 24.455 mins elapsed.

2023-03-09 23:09:22 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (11 of 23)!, 24.503 mins elapsed.

2023-03-09 23:09:25 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (12 of 23)!, 24.552 mins elapsed.

2023-03-09 23:09:29 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (13 of 23)!, 24.619 mins elapsed.

2023-03-09 23:09:32 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (14 of 23)!, 24.665 mins elapsed.

2023-03-09 23:09:34 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (15 of 23)!, 24.713 mins elapsed.

2023-03-09 23:09:38 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (16 of 23)!, 24.78 mins elapsed.

2023-03-09 23:09:41 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (17 of 23)!, 24.828 mins elapsed.

2023-03-09 23:09:45 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (18 of 23)!, 24.887 mins elapsed.

2023-03-09 23:09:49 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (19 of 23)!, 24.954 mins elapsed.

2023-03-09 23:09:52 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (20 of 23)!, 25.003 mins elapsed.

2023-03-09 23:09:55 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (21 of 23)!, 25.049 mins elapsed.

2023-03-09 23:09:59 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (22 of 23)!, 25.115 mins elapsed.

2023-03-09 23:10:01 : Adding BHF_F_Hea11933673_BHF_F_Hea11596626 to GeneExpressionMatrix for Chr (23 of 23)!, 25.163 mins elapsed.

2023-03-09 23:10:09 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (1 of 23)!, 25.282 mins elapsed.

2023-03-09 23:10:12 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (2 of 23)!, 25.338 mins elapsed.

2023-03-09 23:10:15 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (3 of 23)!, 25.393 mins elapsed.

2023-03-09 23:10:20 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (4 of 23)!, 25.466 mins elapsed.

2023-03-09 23:10:23 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (5 of 23)!, 25.517 mins elapsed.

2023-03-09 23:10:26 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (6 of 23)!, 25.569 mins elapsed.

2023-03-09 23:10:31 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (7 of 23)!, 25.657 mins elapsed.

2023-03-09 23:10:35 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (8 of 23)!, 25.72 mins elapsed.

2023-03-09 23:10:38 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (9 of 23)!, 25.772 mins elapsed.

2023-03-09 23:10:43 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (10 of 23)!, 25.85 mins elapsed.

2023-03-09 23:10:46 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (11 of 23)!, 25.902 mins elapsed.

2023-03-09 23:10:49 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (12 of 23)!, 25.954 mins elapsed.

2023-03-09 23:10:53 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (13 of 23)!, 26.026 mins elapsed.

2023-03-09 23:10:56 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (14 of 23)!, 26.075 mins elapsed.

2023-03-09 23:10:59 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (15 of 23)!, 26.126 mins elapsed.

2023-03-09 23:11:03 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (16 of 23)!, 26.196 mins elapsed.

2023-03-09 23:11:06 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (17 of 23)!, 26.246 mins elapsed.

2023-03-09 23:11:10 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (18 of 23)!, 26.306 mins elapsed.

2023-03-09 23:11:15 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (19 of 23)!, 26.391 mins elapsed.

2023-03-09 23:11:19 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (20 of 23)!, 26.45 mins elapsed.

2023-03-09 23:11:22 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (21 of 23)!, 26.499 mins elapsed.

2023-03-09 23:11:26 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (22 of 23)!, 26.569 mins elapsed.

2023-03-09 23:11:29 : Adding BHF_F_Hea13168899_BHF_F_Hea13168515 to GeneExpressionMatrix for Chr (23 of 23)!, 26.616 mins elapsed.

2023-03-09 23:11:37 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (1 of 23)!, 26.749 mins elapsed.

2023-03-09 23:11:40 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (2 of 23)!, 26.808 mins elapsed.

2023-03-09 23:11:43 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (3 of 23)!, 26.857 mins elapsed.

2023-03-09 23:11:48 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (4 of 23)!, 26.931 mins elapsed.

2023-03-09 23:11:51 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (5 of 23)!, 26.989 mins elapsed.

2023-03-09 23:11:55 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (6 of 23)!, 27.05 mins elapsed.

2023-03-09 23:11:59 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (7 of 23)!, 27.123 mins elapsed.

2023-03-09 23:12:02 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (8 of 23)!, 27.171 mins elapsed.

2023-03-09 23:12:05 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (9 of 23)!, 27.217 mins elapsed.

2023-03-09 23:12:09 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (10 of 23)!, 27.285 mins elapsed.

2023-03-09 23:12:12 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (11 of 23)!, 27.332 mins elapsed.

2023-03-09 23:12:14 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (12 of 23)!, 27.379 mins elapsed.

2023-03-09 23:12:19 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (13 of 23)!, 27.447 mins elapsed.

2023-03-09 23:12:21 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (14 of 23)!, 27.493 mins elapsed.

2023-03-09 23:12:24 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (15 of 23)!, 27.541 mins elapsed.

2023-03-09 23:12:28 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (16 of 23)!, 27.609 mins elapsed.

2023-03-09 23:12:31 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (17 of 23)!, 27.657 mins elapsed.

2023-03-09 23:12:34 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (18 of 23)!, 27.705 mins elapsed.

2023-03-09 23:12:38 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (19 of 23)!, 27.772 mins elapsed.

2023-03-09 23:12:41 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (20 of 23)!, 27.821 mins elapsed.

2023-03-09 23:12:44 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (21 of 23)!, 27.867 mins elapsed.

2023-03-09 23:12:48 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (22 of 23)!, 27.932 mins elapsed.

2023-03-09 23:12:50 : Adding BHF_F_Hea11933672_BHF_F_Hea11596625 to GeneExpressionMatrix for Chr (23 of 23)!, 27.978 mins elapsed.

2023-03-09 23:12:59 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (1 of 23)!, 28.118 mins elapsed.

2023-03-09 23:13:02 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (2 of 23)!, 28.172 mins elapsed.

2023-03-09 23:13:05 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (3 of 23)!, 28.224 mins elapsed.

2023-03-09 23:13:09 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (4 of 23)!, 28.296 mins elapsed.

2023-03-09 23:13:12 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (5 of 23)!, 28.344 mins elapsed.

2023-03-09 23:13:15 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (6 of 23)!, 28.393 mins elapsed.

2023-03-09 23:13:19 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (7 of 23)!, 28.463 mins elapsed.

2023-03-09 23:13:22 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (8 of 23)!, 28.513 mins elapsed.

2023-03-09 23:13:25 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (9 of 23)!, 28.562 mins elapsed.

2023-03-09 23:13:30 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (10 of 23)!, 28.636 mins elapsed.

2023-03-09 23:13:33 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (11 of 23)!, 28.686 mins elapsed.

2023-03-09 23:13:36 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (12 of 23)!, 28.735 mins elapsed.

2023-03-09 23:13:40 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (13 of 23)!, 28.807 mins elapsed.

2023-03-09 23:13:43 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (14 of 23)!, 28.856 mins elapsed.

2023-03-09 23:13:46 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (15 of 23)!, 28.906 mins elapsed.

2023-03-09 23:13:50 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (16 of 23)!, 28.979 mins elapsed.

2023-03-09 23:13:53 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (17 of 23)!, 29.03 mins elapsed.

2023-03-09 23:13:57 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (18 of 23)!, 29.081 mins elapsed.

2023-03-09 23:14:01 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (19 of 23)!, 29.149 mins elapsed.

2023-03-09 23:14:04 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (20 of 23)!, 29.201 mins elapsed.

2023-03-09 23:14:07 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (21 of 23)!, 29.247 mins elapsed.

2023-03-09 23:14:11 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (22 of 23)!, 29.324 mins elapsed.

2023-03-09 23:14:15 : Adding BHF_F_Hea13168897_BHF_F_Hea13168513 to GeneExpressionMatrix for Chr (23 of 23)!, 29.383 mins elapsed.

2023-03-09 23:14:21 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (1 of 23)!, 29.494 mins elapsed.

2023-03-09 23:14:24 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (2 of 23)!, 29.546 mins elapsed.

2023-03-09 23:14:27 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (3 of 23)!, 29.594 mins elapsed.

2023-03-09 23:14:31 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (4 of 23)!, 29.663 mins elapsed.

2023-03-09 23:14:34 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (5 of 23)!, 29.71 mins elapsed.

2023-03-09 23:14:37 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (6 of 23)!, 29.758 mins elapsed.

2023-03-09 23:14:41 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (7 of 23)!, 29.825 mins elapsed.

2023-03-09 23:14:44 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (8 of 23)!, 29.876 mins elapsed.

2023-03-09 23:14:47 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (9 of 23)!, 29.925 mins elapsed.

2023-03-09 23:14:51 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (10 of 23)!, 29.992 mins elapsed.

2023-03-09 23:14:55 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (11 of 23)!, 30.049 mins elapsed.

2023-03-09 23:14:58 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (12 of 23)!, 30.108 mins elapsed.

2023-03-09 23:15:03 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (13 of 23)!, 30.191 mins elapsed.

2023-03-09 23:15:06 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (14 of 23)!, 30.24 mins elapsed.

2023-03-09 23:15:09 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (15 of 23)!, 30.287 mins elapsed.

2023-03-09 23:15:14 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (16 of 23)!, 30.372 mins elapsed.

2023-03-09 23:15:17 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (17 of 23)!, 30.429 mins elapsed.

2023-03-09 23:15:21 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (18 of 23)!, 30.488 mins elapsed.

2023-03-09 23:15:26 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (19 of 23)!, 30.57 mins elapsed.

2023-03-09 23:15:29 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (20 of 23)!, 30.618 mins elapsed.

2023-03-09 23:15:32 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (21 of 23)!, 30.669 mins elapsed.

2023-03-09 23:15:36 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (22 of 23)!, 30.738 mins elapsed.

2023-03-09 23:15:39 : Adding BHF_F_Hea11933670_BHF_F_Hea11596623 to GeneExpressionMatrix for Chr (23 of 23)!, 30.786 mins elapsed.

2023-03-09 23:15:46 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (1 of 23)!, 30.906 mins elapsed.

2023-03-09 23:15:49 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (2 of 23)!, 30.956 mins elapsed.

2023-03-09 23:15:52 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (3 of 23)!, 31.006 mins elapsed.

2023-03-09 23:15:56 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (4 of 23)!, 31.073 mins elapsed.

2023-03-09 23:15:59 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (5 of 23)!, 31.12 mins elapsed.

2023-03-09 23:16:02 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (6 of 23)!, 31.167 mins elapsed.

2023-03-09 23:16:06 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (7 of 23)!, 31.234 mins elapsed.

2023-03-09 23:16:09 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (8 of 23)!, 31.281 mins elapsed.

2023-03-09 23:16:11 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (9 of 23)!, 31.327 mins elapsed.

2023-03-09 23:16:15 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (10 of 23)!, 31.392 mins elapsed.

2023-03-09 23:16:18 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (11 of 23)!, 31.439 mins elapsed.

2023-03-09 23:16:21 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (12 of 23)!, 31.486 mins elapsed.

2023-03-09 23:16:25 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (13 of 23)!, 31.552 mins elapsed.

2023-03-09 23:16:28 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (14 of 23)!, 31.597 mins elapsed.

2023-03-09 23:16:30 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (15 of 23)!, 31.643 mins elapsed.

2023-03-09 23:16:34 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (16 of 23)!, 31.71 mins elapsed.

2023-03-09 23:16:37 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (17 of 23)!, 31.757 mins elapsed.

2023-03-09 23:16:40 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (18 of 23)!, 31.804 mins elapsed.

2023-03-09 23:16:44 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (19 of 23)!, 31.868 mins elapsed.

2023-03-09 23:16:47 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (20 of 23)!, 31.915 mins elapsed.

2023-03-09 23:16:49 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (21 of 23)!, 31.96 mins elapsed.

2023-03-09 23:16:53 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (22 of 23)!, 32.028 mins elapsed.

2023-03-09 23:16:56 : Adding 7089STDY13216926_BHF_F_Hea13242533 to GeneExpressionMatrix for Chr (23 of 23)!, 32.075 mins elapsed.

2023-03-09 23:17:03 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (1 of 23)!, 32.181 mins elapsed.

2023-03-09 23:17:06 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (2 of 23)!, 32.232 mins elapsed.

2023-03-09 23:17:09 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (3 of 23)!, 32.281 mins elapsed.

2023-03-09 23:17:13 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (4 of 23)!, 32.358 mins elapsed.

2023-03-09 23:17:16 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (5 of 23)!, 32.407 mins elapsed.

2023-03-09 23:17:19 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (6 of 23)!, 32.463 mins elapsed.

2023-03-09 23:17:24 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (7 of 23)!, 32.533 mins elapsed.

2023-03-09 23:17:27 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (8 of 23)!, 32.583 mins elapsed.

2023-03-09 23:17:30 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (9 of 23)!, 32.631 mins elapsed.

2023-03-09 23:17:34 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (10 of 23)!, 32.697 mins elapsed.

2023-03-09 23:17:36 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (11 of 23)!, 32.744 mins elapsed.

2023-03-09 23:17:39 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (12 of 23)!, 32.792 mins elapsed.

2023-03-09 23:17:43 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (13 of 23)!, 32.859 mins elapsed.

2023-03-09 23:17:46 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (14 of 23)!, 32.906 mins elapsed.

2023-03-09 23:17:49 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (15 of 23)!, 32.954 mins elapsed.

2023-03-09 23:17:53 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (16 of 23)!, 33.021 mins elapsed.

2023-03-09 23:17:56 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (17 of 23)!, 33.072 mins elapsed.

2023-03-09 23:17:59 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (18 of 23)!, 33.121 mins elapsed.

2023-03-09 23:18:03 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (19 of 23)!, 33.189 mins elapsed.

2023-03-09 23:18:06 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (20 of 23)!, 33.237 mins elapsed.

2023-03-09 23:18:09 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (21 of 23)!, 33.285 mins elapsed.

2023-03-09 23:18:13 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (22 of 23)!, 33.352 mins elapsed.

2023-03-09 23:18:16 : Adding BHF_F_Hea11933671_BHF_F_Hea11596624 to GeneExpressionMatrix for Chr (23 of 23)!, 33.398 mins elapsed.

2023-03-09 23:18:22 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (1 of 23)!, 33.506 mins elapsed.

2023-03-09 23:18:25 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (2 of 23)!, 33.558 mins elapsed.

2023-03-09 23:18:29 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (3 of 23)!, 33.614 mins elapsed.

2023-03-09 23:18:33 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (4 of 23)!, 33.682 mins elapsed.

2023-03-09 23:18:35 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (5 of 23)!, 33.729 mins elapsed.

2023-03-09 23:18:38 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (6 of 23)!, 33.777 mins elapsed.

2023-03-09 23:18:42 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (7 of 23)!, 33.844 mins elapsed.

2023-03-09 23:18:45 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (8 of 23)!, 33.897 mins elapsed.

2023-03-09 23:18:48 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (9 of 23)!, 33.944 mins elapsed.

2023-03-09 23:18:52 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (10 of 23)!, 34.012 mins elapsed.

2023-03-09 23:18:55 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (11 of 23)!, 34.06 mins elapsed.

2023-03-09 23:18:58 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (12 of 23)!, 34.113 mins elapsed.

2023-03-09 23:19:03 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (13 of 23)!, 34.181 mins elapsed.

2023-03-09 23:19:05 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (14 of 23)!, 34.227 mins elapsed.

2023-03-09 23:19:08 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (15 of 23)!, 34.273 mins elapsed.

2023-03-09 23:19:12 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (16 of 23)!, 34.338 mins elapsed.

2023-03-09 23:19:15 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (17 of 23)!, 34.385 mins elapsed.

2023-03-09 23:19:18 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (18 of 23)!, 34.432 mins elapsed.

2023-03-09 23:19:22 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (19 of 23)!, 34.499 mins elapsed.

2023-03-09 23:19:25 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (20 of 23)!, 34.548 mins elapsed.

2023-03-09 23:19:27 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (21 of 23)!, 34.594 mins elapsed.

2023-03-09 23:19:32 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (22 of 23)!, 34.668 mins elapsed.

2023-03-09 23:19:35 : Adding BHF_F_Hea11064672_BHF_F_Hea11031825 to GeneExpressionMatrix for Chr (23 of 23)!, 34.715 mins elapsed.

2023-03-09 23:19:41 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (1 of 23)!, 34.818 mins elapsed.

2023-03-09 23:19:44 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (2 of 23)!, 34.867 mins elapsed.

2023-03-09 23:19:47 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (3 of 23)!, 34.914 mins elapsed.

2023-03-09 23:19:51 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (4 of 23)!, 34.996 mins elapsed.

2023-03-09 23:19:55 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (5 of 23)!, 35.055 mins elapsed.

2023-03-09 23:19:58 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (6 of 23)!, 35.113 mins elapsed.

2023-03-09 23:20:02 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (7 of 23)!, 35.179 mins elapsed.

2023-03-09 23:20:05 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (8 of 23)!, 35.226 mins elapsed.

2023-03-09 23:20:08 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (9 of 23)!, 35.275 mins elapsed.

2023-03-09 23:20:12 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (10 of 23)!, 35.342 mins elapsed.

2023-03-09 23:20:15 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (11 of 23)!, 35.392 mins elapsed.

2023-03-09 23:20:18 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (12 of 23)!, 35.438 mins elapsed.

2023-03-09 23:20:22 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (13 of 23)!, 35.505 mins elapsed.

2023-03-09 23:20:25 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (14 of 23)!, 35.562 mins elapsed.

2023-03-09 23:20:28 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (15 of 23)!, 35.609 mins elapsed.

2023-03-09 23:20:32 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (16 of 23)!, 35.674 mins elapsed.

2023-03-09 23:20:35 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (17 of 23)!, 35.72 mins elapsed.

2023-03-09 23:20:38 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (18 of 23)!, 35.768 mins elapsed.

2023-03-09 23:20:42 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (19 of 23)!, 35.834 mins elapsed.

2023-03-09 23:20:45 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (20 of 23)!, 35.892 mins elapsed.

2023-03-09 23:20:48 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (21 of 23)!, 35.942 mins elapsed.

2023-03-09 23:20:52 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (22 of 23)!, 36.008 mins elapsed.

2023-03-09 23:20:55 : Adding 7089STDY13216922_BHF_F_Hea13242529 to GeneExpressionMatrix for Chr (23 of 23)!, 36.063 mins elapsed.

2023-03-09 23:21:02 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (1 of 23)!, 36.168 mins elapsed.

2023-03-09 23:21:05 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (2 of 23)!, 36.216 mins elapsed.

2023-03-09 23:21:07 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (3 of 23)!, 36.263 mins elapsed.

2023-03-09 23:21:11 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (4 of 23)!, 36.329 mins elapsed.

2023-03-09 23:21:14 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (5 of 23)!, 36.378 mins elapsed.

2023-03-09 23:21:17 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (6 of 23)!, 36.427 mins elapsed.

2023-03-09 23:21:22 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (7 of 23)!, 36.509 mins elapsed.

2023-03-09 23:21:26 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (8 of 23)!, 36.564 mins elapsed.

2023-03-09 23:21:28 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (9 of 23)!, 36.61 mins elapsed.

2023-03-09 23:21:32 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (10 of 23)!, 36.679 mins elapsed.

2023-03-09 23:21:35 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (11 of 23)!, 36.726 mins elapsed.

2023-03-09 23:21:38 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (12 of 23)!, 36.773 mins elapsed.

2023-03-09 23:21:42 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (13 of 23)!, 36.841 mins elapsed.

2023-03-09 23:21:45 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (14 of 23)!, 36.888 mins elapsed.

2023-03-09 23:21:48 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (15 of 23)!, 36.936 mins elapsed.

2023-03-09 23:21:52 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (16 of 23)!, 37.003 mins elapsed.

2023-03-09 23:21:55 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (17 of 23)!, 37.05 mins elapsed.

2023-03-09 23:21:58 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (18 of 23)!, 37.098 mins elapsed.

2023-03-09 23:22:02 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (19 of 23)!, 37.167 mins elapsed.

2023-03-09 23:22:05 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (20 of 23)!, 37.214 mins elapsed.

2023-03-09 23:22:07 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (21 of 23)!, 37.26 mins elapsed.

2023-03-09 23:22:11 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (22 of 23)!, 37.325 mins elapsed.

2023-03-09 23:22:14 : Adding BHF_F_Hea13188317_BHF_F_Hea13187619 to GeneExpressionMatrix for Chr (23 of 23)!, 37.372 mins elapsed.

2023-03-09 23:22:20 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (1 of 23)!, 37.476 mins elapsed.

2023-03-09 23:22:23 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (2 of 23)!, 37.525 mins elapsed.

2023-03-09 23:22:26 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (3 of 23)!, 37.574 mins elapsed.

2023-03-09 23:22:30 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (4 of 23)!, 37.642 mins elapsed.

2023-03-09 23:22:33 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (5 of 23)!, 37.689 mins elapsed.

2023-03-09 23:22:36 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (6 of 23)!, 37.736 mins elapsed.

2023-03-09 23:22:40 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (7 of 23)!, 37.803 mins elapsed.

2023-03-09 23:22:43 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (8 of 23)!, 37.85 mins elapsed.

2023-03-09 23:22:46 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (9 of 23)!, 37.898 mins elapsed.

2023-03-09 23:22:50 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (10 of 23)!, 37.965 mins elapsed.

2023-03-09 23:22:52 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (11 of 23)!, 38.013 mins elapsed.

2023-03-09 23:22:55 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (12 of 23)!, 38.06 mins elapsed.

2023-03-09 23:22:59 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (13 of 23)!, 38.129 mins elapsed.

2023-03-09 23:23:02 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (14 of 23)!, 38.175 mins elapsed.

2023-03-09 23:23:05 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (15 of 23)!, 38.223 mins elapsed.

2023-03-09 23:23:09 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (16 of 23)!, 38.29 mins elapsed.

2023-03-09 23:23:12 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (17 of 23)!, 38.338 mins elapsed.

2023-03-09 23:23:15 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (18 of 23)!, 38.388 mins elapsed.

2023-03-09 23:23:19 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (19 of 23)!, 38.453 mins elapsed.

2023-03-09 23:23:22 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (20 of 23)!, 38.5 mins elapsed.

2023-03-09 23:23:25 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (21 of 23)!, 38.548 mins elapsed.

2023-03-09 23:23:29 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (22 of 23)!, 38.617 mins elapsed.

2023-03-09 23:23:32 : Adding BHF_F_Hea13168893_BHF_F_Hea13168509 to GeneExpressionMatrix for Chr (23 of 23)!, 38.664 mins elapsed.

2023-03-09 23:23:38 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (1 of 23)!, 38.772 mins elapsed.

2023-03-09 23:23:41 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (2 of 23)!, 38.83 mins elapsed.

2023-03-09 23:23:45 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (3 of 23)!, 38.891 mins elapsed.

2023-03-09 23:23:50 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (4 of 23)!, 38.965 mins elapsed.

2023-03-09 23:23:52 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (5 of 23)!, 39.013 mins elapsed.

2023-03-09 23:23:55 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (6 of 23)!, 39.061 mins elapsed.

2023-03-09 23:23:59 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (7 of 23)!, 39.127 mins elapsed.

2023-03-09 23:24:02 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (8 of 23)!, 39.175 mins elapsed.

2023-03-09 23:24:05 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (9 of 23)!, 39.222 mins elapsed.

2023-03-09 23:24:10 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (10 of 23)!, 39.298 mins elapsed.

2023-03-09 23:24:12 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (11 of 23)!, 39.346 mins elapsed.

2023-03-09 23:24:16 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (12 of 23)!, 39.403 mins elapsed.

2023-03-09 23:24:20 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (13 of 23)!, 39.471 mins elapsed.

2023-03-09 23:24:23 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (14 of 23)!, 39.517 mins elapsed.

2023-03-09 23:24:25 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (15 of 23)!, 39.563 mins elapsed.

2023-03-09 23:24:30 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (16 of 23)!, 39.637 mins elapsed.

2023-03-09 23:24:33 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (17 of 23)!, 39.684 mins elapsed.

2023-03-09 23:24:36 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (18 of 23)!, 39.732 mins elapsed.

2023-03-09 23:24:40 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (19 of 23)!, 39.809 mins elapsed.

2023-03-09 23:24:44 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (20 of 23)!, 39.868 mins elapsed.

2023-03-09 23:24:47 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (21 of 23)!, 39.917 mins elapsed.

2023-03-09 23:24:51 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (22 of 23)!, 39.988 mins elapsed.

2023-03-09 23:24:54 : Adding BHF_F_Hea11933674_BHF_F_Hea11596627 to GeneExpressionMatrix for Chr (23 of 23)!, 40.035 mins elapsed.

2023-03-09 23:25:01 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (1 of 23)!, 40.156 mins elapsed.

2023-03-09 23:25:04 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (2 of 23)!, 40.205 mins elapsed.

2023-03-09 23:25:08 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (3 of 23)!, 40.265 mins elapsed.

2023-03-09 23:25:12 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (4 of 23)!, 40.337 mins elapsed.

2023-03-09 23:25:15 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (5 of 23)!, 40.391 mins elapsed.

2023-03-09 23:25:18 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (6 of 23)!, 40.441 mins elapsed.

2023-03-09 23:25:22 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (7 of 23)!, 40.509 mins elapsed.

2023-03-09 23:25:26 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (8 of 23)!, 40.569 mins elapsed.

2023-03-09 23:25:29 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (9 of 23)!, 40.628 mins elapsed.

2023-03-09 23:25:34 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (10 of 23)!, 40.697 mins elapsed.

2023-03-09 23:25:36 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (11 of 23)!, 40.745 mins elapsed.

2023-03-09 23:25:39 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (12 of 23)!, 40.794 mins elapsed.

2023-03-09 23:25:43 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (13 of 23)!, 40.863 mins elapsed.

2023-03-09 23:25:46 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (14 of 23)!, 40.91 mins elapsed.

2023-03-09 23:25:49 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (15 of 23)!, 40.957 mins elapsed.

2023-03-09 23:25:53 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (16 of 23)!, 41.024 mins elapsed.

2023-03-09 23:25:56 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (17 of 23)!, 41.072 mins elapsed.

2023-03-09 23:25:59 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (18 of 23)!, 41.12 mins elapsed.

2023-03-09 23:26:03 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (19 of 23)!, 41.186 mins elapsed.

2023-03-09 23:26:06 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (20 of 23)!, 41.236 mins elapsed.

2023-03-09 23:26:09 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (21 of 23)!, 41.284 mins elapsed.

2023-03-09 23:26:13 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (22 of 23)!, 41.351 mins elapsed.

2023-03-09 23:26:16 : Adding BHF_F_Hea13168892_BHF_F_Hea13168508 to GeneExpressionMatrix for Chr (23 of 23)!, 41.398 mins elapsed.

2023-03-09 23:26:23 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (1 of 23)!, 41.518 mins elapsed.

2023-03-09 23:26:26 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (2 of 23)!, 41.577 mins elapsed.

2023-03-09 23:26:29 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (3 of 23)!, 41.629 mins elapsed.

2023-03-09 23:26:34 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (4 of 23)!, 41.698 mins elapsed.

2023-03-09 23:26:36 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (5 of 23)!, 41.746 mins elapsed.

2023-03-09 23:26:40 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (6 of 23)!, 41.798 mins elapsed.

2023-03-09 23:26:44 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (7 of 23)!, 41.875 mins elapsed.

2023-03-09 23:26:47 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (8 of 23)!, 41.925 mins elapsed.

2023-03-09 23:26:51 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (9 of 23)!, 41.982 mins elapsed.

2023-03-09 23:26:55 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (10 of 23)!, 42.05 mins elapsed.

2023-03-09 23:26:58 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (11 of 23)!, 42.098 mins elapsed.

2023-03-09 23:27:00 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (12 of 23)!, 42.146 mins elapsed.

2023-03-09 23:27:05 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (13 of 23)!, 42.214 mins elapsed.

2023-03-09 23:27:07 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (14 of 23)!, 42.26 mins elapsed.

2023-03-09 23:27:10 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (15 of 23)!, 42.313 mins elapsed.

2023-03-09 23:27:15 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (16 of 23)!, 42.381 mins elapsed.

2023-03-09 23:27:17 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (17 of 23)!, 42.429 mins elapsed.

2023-03-09 23:27:20 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (18 of 23)!, 42.479 mins elapsed.

2023-03-09 23:27:24 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (19 of 23)!, 42.545 mins elapsed.

2023-03-09 23:27:27 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (20 of 23)!, 42.593 mins elapsed.

2023-03-09 23:27:30 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (21 of 23)!, 42.643 mins elapsed.

2023-03-09 23:27:35 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (22 of 23)!, 42.726 mins elapsed.

2023-03-09 23:27:39 : Adding BHF_F_Hea11064671_BHF_F_Hea11031824 to GeneExpressionMatrix for Chr (23 of 23)!, 42.781 mins elapsed.

2023-03-09 23:27:46 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (1 of 23)!, 42.902 mins elapsed.

2023-03-09 23:27:49 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (2 of 23)!, 42.952 mins elapsed.

2023-03-09 23:27:52 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (3 of 23)!, 42.999 mins elapsed.

2023-03-09 23:27:56 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (4 of 23)!, 43.065 mins elapsed.

2023-03-09 23:27:59 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (5 of 23)!, 43.121 mins elapsed.

2023-03-09 23:28:02 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (6 of 23)!, 43.177 mins elapsed.

2023-03-09 23:28:07 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (7 of 23)!, 43.259 mins elapsed.

2023-03-09 23:28:10 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (8 of 23)!, 43.313 mins elapsed.

2023-03-09 23:28:13 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (9 of 23)!, 43.36 mins elapsed.

2023-03-09 23:28:17 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (10 of 23)!, 43.426 mins elapsed.

2023-03-09 23:28:20 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (11 of 23)!, 43.471 mins elapsed.

2023-03-09 23:28:23 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (12 of 23)!, 43.517 mins elapsed.

2023-03-09 23:28:27 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (13 of 23)!, 43.584 mins elapsed.

2023-03-09 23:28:29 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (14 of 23)!, 43.629 mins elapsed.

2023-03-09 23:28:32 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (15 of 23)!, 43.676 mins elapsed.

2023-03-09 23:28:36 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (16 of 23)!, 43.745 mins elapsed.

2023-03-09 23:28:39 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (17 of 23)!, 43.796 mins elapsed.

2023-03-09 23:28:42 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (18 of 23)!, 43.843 mins elapsed.

2023-03-09 23:28:46 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (19 of 23)!, 43.911 mins elapsed.

2023-03-09 23:28:49 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (20 of 23)!, 43.957 mins elapsed.

2023-03-09 23:28:52 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (21 of 23)!, 44.004 mins elapsed.

2023-03-09 23:28:56 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (22 of 23)!, 44.071 mins elapsed.

2023-03-09 23:28:59 : Adding BHF_F_Hea13188328_BHF_F_Hea13187630 to GeneExpressionMatrix for Chr (23 of 23)!, 44.118 mins elapsed.

2023-03-09 23:29:06 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (1 of 23)!, 44.231 mins elapsed.

2023-03-09 23:29:08 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (2 of 23)!, 44.277 mins elapsed.

2023-03-09 23:29:11 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (3 of 23)!, 44.323 mins elapsed.

2023-03-09 23:29:15 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (4 of 23)!, 44.393 mins elapsed.

2023-03-09 23:29:18 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (5 of 23)!, 44.44 mins elapsed.

2023-03-09 23:29:21 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (6 of 23)!, 44.488 mins elapsed.

2023-03-09 23:29:26 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (7 of 23)!, 44.568 mins elapsed.

2023-03-09 23:29:29 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (8 of 23)!, 44.62 mins elapsed.

2023-03-09 23:29:32 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (9 of 23)!, 44.665 mins elapsed.

2023-03-09 23:29:35 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (10 of 23)!, 44.729 mins elapsed.

2023-03-09 23:29:38 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (11 of 23)!, 44.775 mins elapsed.

2023-03-09 23:29:41 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (12 of 23)!, 44.82 mins elapsed.

2023-03-09 23:29:45 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (13 of 23)!, 44.885 mins elapsed.

2023-03-09 23:29:48 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (14 of 23)!, 44.932 mins elapsed.

2023-03-09 23:29:50 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (15 of 23)!, 44.978 mins elapsed.

2023-03-09 23:29:54 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (16 of 23)!, 45.044 mins elapsed.

2023-03-09 23:29:57 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (17 of 23)!, 45.089 mins elapsed.

2023-03-09 23:30:00 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (18 of 23)!, 45.136 mins elapsed.

2023-03-09 23:30:04 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (19 of 23)!, 45.202 mins elapsed.

2023-03-09 23:30:07 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (20 of 23)!, 45.248 mins elapsed.

2023-03-09 23:30:09 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (21 of 23)!, 45.294 mins elapsed.

2023-03-09 23:30:13 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (22 of 23)!, 45.359 mins elapsed.

2023-03-09 23:30:16 : Adding BHF_F_Hea13188329_BHF_F_Hea13187631 to GeneExpressionMatrix for Chr (23 of 23)!, 45.405 mins elapsed.

2023-03-09 23:30:22 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (1 of 23)!, 45.504 mins elapsed.

2023-03-09 23:30:25 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (2 of 23)!, 45.55 mins elapsed.

2023-03-09 23:30:27 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (3 of 23)!, 45.596 mins elapsed.

2023-03-09 23:30:31 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (4 of 23)!, 45.661 mins elapsed.

2023-03-09 23:30:34 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (5 of 23)!, 45.707 mins elapsed.

2023-03-09 23:30:37 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (6 of 23)!, 45.753 mins elapsed.

2023-03-09 23:30:41 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (7 of 23)!, 45.818 mins elapsed.

2023-03-09 23:30:44 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (8 of 23)!, 45.864 mins elapsed.

2023-03-09 23:30:46 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (9 of 23)!, 45.909 mins elapsed.

2023-03-09 23:30:50 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (10 of 23)!, 45.976 mins elapsed.

2023-03-09 23:30:53 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (11 of 23)!, 46.022 mins elapsed.

2023-03-09 23:30:56 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (12 of 23)!, 46.068 mins elapsed.

2023-03-09 23:31:00 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (13 of 23)!, 46.134 mins elapsed.

2023-03-09 23:31:03 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (14 of 23)!, 46.181 mins elapsed.

2023-03-09 23:31:05 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (15 of 23)!, 46.227 mins elapsed.

2023-03-09 23:31:09 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (16 of 23)!, 46.294 mins elapsed.

2023-03-09 23:31:12 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (17 of 23)!, 46.34 mins elapsed.

2023-03-09 23:31:15 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (18 of 23)!, 46.387 mins elapsed.

2023-03-09 23:31:19 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (19 of 23)!, 46.457 mins elapsed.

2023-03-09 23:31:22 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (20 of 23)!, 46.503 mins elapsed.

2023-03-09 23:31:25 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (21 of 23)!, 46.549 mins elapsed.

2023-03-09 23:31:29 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (22 of 23)!, 46.615 mins elapsed.

2023-03-09 23:31:31 : Adding BHF_F_Hea13188330_BHF_F_Hea13187632 to GeneExpressionMatrix for Chr (23 of 23)!, 46.66 mins elapsed.

2023-03-09 23:31:37 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (1 of 23)!, 46.76 mins elapsed.

2023-03-09 23:31:40 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (2 of 23)!, 46.806 mins elapsed.

2023-03-09 23:31:43 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (3 of 23)!, 46.852 mins elapsed.

2023-03-09 23:31:47 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (4 of 23)!, 46.917 mins elapsed.

2023-03-09 23:31:49 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (5 of 23)!, 46.962 mins elapsed.

2023-03-09 23:31:52 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (6 of 23)!, 47.007 mins elapsed.

2023-03-09 23:31:56 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (7 of 23)!, 47.073 mins elapsed.

2023-03-09 23:31:59 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (8 of 23)!, 47.118 mins elapsed.

2023-03-09 23:32:01 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (9 of 23)!, 47.163 mins elapsed.

2023-03-09 23:32:05 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (10 of 23)!, 47.228 mins elapsed.

2023-03-09 23:32:08 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (11 of 23)!, 47.274 mins elapsed.

2023-03-09 23:32:11 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (12 of 23)!, 47.32 mins elapsed.

2023-03-09 23:32:15 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (13 of 23)!, 47.386 mins elapsed.

2023-03-09 23:32:18 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (14 of 23)!, 47.431 mins elapsed.

2023-03-09 23:32:21 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (15 of 23)!, 47.488 mins elapsed.

2023-03-09 23:32:26 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (16 of 23)!, 47.569 mins elapsed.

2023-03-09 23:32:29 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (17 of 23)!, 47.62 mins elapsed.

2023-03-09 23:32:32 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (18 of 23)!, 47.668 mins elapsed.

2023-03-09 23:32:36 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (19 of 23)!, 47.737 mins elapsed.

2023-03-09 23:32:39 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (20 of 23)!, 47.783 mins elapsed.

2023-03-09 23:32:41 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (21 of 23)!, 47.829 mins elapsed.

2023-03-09 23:32:45 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (22 of 23)!, 47.895 mins elapsed.

2023-03-09 23:32:48 : Adding BHF_F_Hea11064670_BHF_F_Hea11031823 to GeneExpressionMatrix for Chr (23 of 23)!, 47.94 mins elapsed.

2023-03-09 23:32:54 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (1 of 23)!, 48.039 mins elapsed.

2023-03-09 23:32:57 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (2 of 23)!, 48.085 mins elapsed.

2023-03-09 23:33:00 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (3 of 23)!, 48.136 mins elapsed.

2023-03-09 23:33:04 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (4 of 23)!, 48.2 mins elapsed.

2023-03-09 23:33:07 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (5 of 23)!, 48.254 mins elapsed.

2023-03-09 23:33:10 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (6 of 23)!, 48.31 mins elapsed.

2023-03-09 23:33:14 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (7 of 23)!, 48.375 mins elapsed.

2023-03-09 23:33:17 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (8 of 23)!, 48.419 mins elapsed.

2023-03-09 23:33:19 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (9 of 23)!, 48.463 mins elapsed.

2023-03-09 23:33:23 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (10 of 23)!, 48.527 mins elapsed.

2023-03-09 23:33:26 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (11 of 23)!, 48.572 mins elapsed.

2023-03-09 23:33:29 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (12 of 23)!, 48.617 mins elapsed.

2023-03-09 23:33:33 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (13 of 23)!, 48.694 mins elapsed.

2023-03-09 23:33:36 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (14 of 23)!, 48.742 mins elapsed.

2023-03-09 23:33:39 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (15 of 23)!, 48.787 mins elapsed.

2023-03-09 23:33:43 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (16 of 23)!, 48.852 mins elapsed.

2023-03-09 23:33:46 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (17 of 23)!, 48.897 mins elapsed.

2023-03-09 23:33:48 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (18 of 23)!, 48.946 mins elapsed.

2023-03-09 23:33:52 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (19 of 23)!, 49.012 mins elapsed.

2023-03-09 23:33:55 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (20 of 23)!, 49.056 mins elapsed.

2023-03-09 23:33:58 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (21 of 23)!, 49.101 mins elapsed.

2023-03-09 23:34:02 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (22 of 23)!, 49.166 mins elapsed.

2023-03-09 23:34:04 : Adding BHF_F_Hea11933675_BHF_F_Hea11596628 to GeneExpressionMatrix for Chr (23 of 23)!, 49.211 mins elapsed.

2023-03-09 23:34:10 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (1 of 23)!, 49.308 mins elapsed.

2023-03-09 23:34:13 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (2 of 23)!, 49.353 mins elapsed.

2023-03-09 23:34:15 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (3 of 23)!, 49.397 mins elapsed.

2023-03-09 23:34:20 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (4 of 23)!, 49.468 mins elapsed.

2023-03-09 23:34:22 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (5 of 23)!, 49.513 mins elapsed.

2023-03-09 23:34:25 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (6 of 23)!, 49.557 mins elapsed.

2023-03-09 23:34:29 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (7 of 23)!, 49.621 mins elapsed.

2023-03-09 23:34:32 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (8 of 23)!, 49.665 mins elapsed.

2023-03-09 23:34:34 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (9 of 23)!, 49.71 mins elapsed.

2023-03-09 23:34:38 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (10 of 23)!, 49.773 mins elapsed.

2023-03-09 23:34:41 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (11 of 23)!, 49.818 mins elapsed.

2023-03-09 23:34:44 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (12 of 23)!, 49.873 mins elapsed.

2023-03-09 23:34:49 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (13 of 23)!, 49.954 mins elapsed.

2023-03-09 23:34:52 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (14 of 23)!, 50.002 mins elapsed.

2023-03-09 23:34:55 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (15 of 23)!, 50.048 mins elapsed.

2023-03-09 23:34:58 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (16 of 23)!, 50.112 mins elapsed.

2023-03-09 23:35:01 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (17 of 23)!, 50.157 mins elapsed.

2023-03-09 23:35:04 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (18 of 23)!, 50.202 mins elapsed.

2023-03-09 23:35:08 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (19 of 23)!, 50.272 mins elapsed.

2023-03-09 23:35:11 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (20 of 23)!, 50.319 mins elapsed.

2023-03-09 23:35:14 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (21 of 23)!, 50.365 mins elapsed.

2023-03-09 23:35:18 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (22 of 23)!, 50.43 mins elapsed.

2023-03-09 23:35:20 : Adding 7089STDY13216923_BHF_F_Hea13242530 to GeneExpressionMatrix for Chr (23 of 23)!, 50.475 mins elapsed.

ArchR logging successful to : ArchRLogs/ArchR-addGeneExpressionMatrix-49213027a1f7-Date-2023-03-09_Time-22-44-06.log


           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 31 (unknown):
```unknown
class: ArchRProject 
outputDirectory: /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output 
samples(37): BHF_F_Hea11064670_BHF_F_Hea11031823
  BHF_F_Hea11064671_BHF_F_Hea11031824 ...
  HCAHeartST13386009_HCAHeartST13303419
  HCAHeartST13386010_HCAHeartST13303420
sampleColData names(1): ArrowFiles
cellColData names(63): Sample TSSEnrichment ... Gex_MitoRatio
  Gex_RiboRatio
numberOfCells(1): 167022
medianTSS(1): 11.614
medianFrags(1): 10338.5
```

Example 32 (unknown):
```unknown
saveArchRProject(ArchRProj = proj, outputDirectory = "project_output", load = FALSE)
```

Example 33 (unknown):
```unknown
Saving ArchRProject...
```

---

## Notebook

**URL:** http://127.0.0.1:9020/notebooks_html/Fig1_General_processing/ATAC/ATAC_preprocess/anndata_normPeakMatrix_to_anndata.html

**Contents:**
- Read in¶
- Make anndata¶
- Add cell type annotation¶
- Refine metadata¶

ref: is peak matrix extracted with getMatrixFromProject normalized? NO https://github.com/GreenleafLab/ArchR/discussions/943

508040 rows × 0 columns

167022 rows × 0 columns

167022 rows × 0 columns

**Examples:**

Example 1 (python):
```python
import scanpy as sc
import pandas as pd
import numpy as np
import anndata

from scipy.io import mmwrite, mmread
from scipy.sparse import csr_matrix
```

Example 2 (unknown):
```unknown
!ls -l /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix
```

Example 3 (python):
```python
total 46364348
-rw-r--r-- 1 20383 1000624     1492397 Mar 12 20:40 barcodes.tsv.gz
-rw-r--r-- 1 20383 1000624     4082604 Mar 12 20:40 features.tsv.gz
-rw-r--r-- 1 20383 1000624  3579115352 Mar 19 18:39 Foetal_Cardiomyocytes_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 22:12 Foetal_Cardiomyocytes_peakVI-model
-rw-r--r-- 1 20383 1000624   538152433 Mar 19 18:40 Foetal_Endothelium_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 19:21 Foetal_Endothelium_peakVI-model
-rw-r--r-- 1 20383 1000624   163683392 Mar 19 18:41 Foetal_Epicardium_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 19:29 Foetal_Epicardium_peakVI-model
-rw-r--r-- 1 20383 1000624  1000890284 Mar 19 18:42 Foetal_Leukocytes_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 23:29 Foetal_Leukocytes_peakVI-model
-rw-r--r-- 1 20383 1000624  4253490105 Mar 19 18:48 Foetal_Mesenchymal_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 18:34 Foetal_Mesenchymal_peakVI-model
drwxr-xr-x 1 20383 1000624          26 Mar 25 22:12 Foetal_MP_peakVI-model
-rw-r--r-- 1 20383 1000624   235356930 Mar 19 18:48 Foetal_Neural_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 18:48 Foetal_Neural_peakVI-model
-rw-r--r-- 1 20383 1000624   611045376 Apr  5 13:29 Foetal_Peaks.h5ad
-rw-r--r-- 1 20383 1000624  9477510996 Mar 14 08:12 Foetal_Peaks_post-peakVI.h5ad
-rw-r--r-- 1 20383 1000624  9459770872 Mar 30 16:37 Foetal_Peaks_tfidf.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 14 08:12 Foetal_peakVI-model
-rw-r--r-- 1 20383 1000624  3755691976 Mar 12 20:40 matrix.mtx.gz
-rw-r--r-- 1 20383 1000624 14315705883 Mar 30 13:54 matrix_tfidf.mtx.gz
-rw-r--r-- 1 20383 1000624    81051521 Apr  4 08:21 peak_metadata.tsv
```

Example 4 (unknown):
```unknown
peakmatrix_dir = '/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix'
```

Example 5 (unknown):
```unknown
# peak matrix, not-binarised
mat = mmread(f'{peakmatrix_dir}/matrix_tfidf.mtx.gz')
mat
```

Example 6 (python):
```python
<508040x167022 sparse matrix of type '<class 'numpy.float64'>'
	with 1173033588 stored elements in COOrdinate format>
```

Example 7 (python):
```python
# peak names
features = pd.read_csv(f'{peakmatrix_dir}/features.tsv.gz', header=None, sep='\t')[[0]]
features.set_index(0,inplace=True)
features
```

Example 8 (python):
```python
# cell barcodes
cells = pd.read_csv(f'{peakmatrix_dir}/barcodes.tsv.gz', header=None, sep='\t')[[1]]
cells.set_index(1,inplace=True)
cells
```

Example 9 (python):
```python
adata = anndata.AnnData(
    X=mat.T,
    obs=cells,
    var=features
)

# rename obs_names
adata.obs_names = [x.replace('#','_') for x in adata.obs_names]

# convert sparce matrix
adata.X = adata.X.tocsr()
adata.X
```

Example 10 (python):
```python
<167022x508040 sparse matrix of type '<class 'numpy.float32'>'
	with 1173033588 stored elements in Compressed Sparse Row format>
```

Example 11 (unknown):
```unknown
AnnData object with n_obs × n_vars = 167022 × 508040
```

Example 12 (python):
```python
adata.X.data[:30]
```

Example 13 (unknown):
```unknown
array([1.768611 , 1.9229858, 3.635446 , 1.3192275, 1.4049321, 1.8123279,
       1.6739427, 2.9703567, 3.3852873, 1.2617257, 2.8007214, 0.7237267,
       1.4759332, 3.1692483, 3.266629 , 3.2549186, 3.8324249, 2.7257555,
       3.126333 , 3.7325323, 3.785544 , 4.073427 , 4.067536 , 4.1232815,
       3.4213552, 3.0830379, 3.7987761, 1.0650452, 3.5462437, 0.8590813],
      dtype=float32)
```

Example 14 (python):
```python
np.max(adata.X.data)
```

Example 15 (python):
```python
adata.obs.drop[]
```

Example 16 (python):
```python
obs = pd.read_csv('/nfs/team205/heart/anndata_objects/Foetal/Feb28ObjectRaw.obs.csv',index_col=0)

# add cell type labels and other metadata
metadata_to_add = ['sangerID', 'combinedID', 'donor', 
       'facility', 'cell_or_nuclei', 'modality', 'kit_10x','multiplexed',
        'batch_key','region','FACSgate','sex','week','trimester',
                     'fine_grain','mid_grain','coarse_grain',
                     'heart_or_greatvessels','cycling','S_score','G2M_score','phase']
adata.obs[metadata_to_add] = obs[metadata_to_add].reindex(adata.obs_names).copy()
adata
```

Example 17 (python):
```python
/opt/conda/envs/teichlab/lib/python3.8/site-packages/IPython/core/interactiveshell.py:3165: DtypeWarning: Columns (31) have mixed types.Specify dtype option on import or set low_memory=False.
  has_raised = await self.run_ast_nodes(code_ast.body, cell_name,
```

Example 18 (unknown):
```unknown
AnnData object with n_obs × n_vars = 167022 × 508040
    obs: 'sangerID', 'combinedID', 'donor', 'facility', 'cell_or_nuclei', 'modality', 'kit_10x', 'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'HB_score', 'multiplexed', 'batch_key', 'region', 'FACSgate', 'sex', 'week', 'trimester', 'fine_grain', 'mid_grain', 'coarse_grain', 'heart_or_greatvessels', 'cycling', 'S_score', 'G2M_score', 'phase', 'stress_score', 'hb1_score'
```

Example 19 (python):
```python
adata.obs['modality'] = 'Multiome_ATAC'
```

Example 20 (python):
```python
adata.var.rename_axis('Peaks', axis=0, inplace=True)
```

Example 21 (python):
```python
# save
adata.write(f'{peakmatrix_dir}/Foetal_Peaks_tfidf.h5ad')
```

Example 22 (unknown):
```unknown
... storing 'sangerID' as categorical
... storing 'combinedID' as categorical
... storing 'donor' as categorical
... storing 'facility' as categorical
... storing 'cell_or_nuclei' as categorical
... storing 'modality' as categorical
... storing 'kit_10x' as categorical
... storing 'multiplexed' as categorical
... storing 'batch_key' as categorical
... storing 'region' as categorical
... storing 'FACSgate' as categorical
... storing 'sex' as categorical
... storing 'week' as categorical
... storing 'trimester' as categorical
... storing 'fine_grain' as categorical
... storing 'mid_grain' as categorical
... storing 'coarse_grain' as categorical
... storing 'heart_or_greatvessels' as categorical
... storing 'cycling' as categorical
... storing 'phase' as categorical
```

Example 23 (unknown):
```unknown
!ls -l /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix
```

Example 24 (unknown):
```unknown
total 54926532
-rw-r--r-- 1 20383 1000624     1492397 Mar 12 20:40 barcodes.tsv.gz
-rw-r--r-- 1 20383 1000624     4082604 Mar 12 20:40 features.tsv.gz
-rw-r--r-- 1 20383 1000624  3579115352 Mar 19 18:39 Foetal_Cardiomyocytes_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 22:12 Foetal_Cardiomyocytes_peakVI-model
-rw-r--r-- 1 20383 1000624   538152433 Mar 19 18:40 Foetal_Endothelium_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 19:21 Foetal_Endothelium_peakVI-model
-rw-r--r-- 1 20383 1000624   163683392 Mar 19 18:41 Foetal_Epicardium_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 19:29 Foetal_Epicardium_peakVI-model
-rw-r--r-- 1 20383 1000624  1000890284 Mar 19 18:42 Foetal_Leukocytes_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 23:29 Foetal_Leukocytes_peakVI-model
-rw-r--r-- 1 20383 1000624  4253490105 Mar 19 18:48 Foetal_Mesenchymal_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 18:34 Foetal_Mesenchymal_peakVI-model
drwxr-xr-x 1 20383 1000624          26 Mar 25 22:12 Foetal_MP_peakVI-model
-rw-r--r-- 1 20383 1000624   235356930 Mar 19 18:48 Foetal_Neural_Peaks_post-peakVI.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 15 18:48 Foetal_Neural_peakVI-model
-rw-r--r-- 1 20383 1000624  9459770872 Mar 13 00:38 Foetal_Peaks.h5ad
-rw-r--r-- 1 20383 1000624  9477510996 Mar 14 08:12 Foetal_Peaks_post-peakVI.h5ad
-rw-r--r-- 1 20383 1000624  9459770872 Mar 30 16:37 Foetal_Peaks_tfidf.h5ad
drwxr-xr-x 1 20383 1000624          26 Mar 14 08:12 Foetal_peakVI-model
-rw-r--r-- 1 20383 1000624  3755691976 Mar 12 20:40 matrix.mtx.gz
-rw-r--r-- 1 20383 1000624 14315705883 Mar 30 13:54 matrix_tfidf.mtx.gz
```

Example 25 (python):
```python
adata_test = sc.read_h5ad(f'{peakmatrix_dir}/Foetal_Peaks_tfidf.h5ad')
adata_test
```

Example 26 (unknown):
```unknown
AnnData object with n_obs × n_vars = 167022 × 508040
    obs: 'sangerID', 'combinedID', 'donor', 'facility', 'cell_or_nuclei', 'modality', 'kit_10x', 'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'HB_score', 'multiplexed', 'batch_key', 'region', 'FACSgate', 'sex', 'week', 'trimester', 'fine_grain', 'mid_grain', 'coarse_grain', 'heart_or_greatvessels', 'cycling', 'S_score', 'G2M_score', 'phase', 'stress_score', 'hb1_score'
```

Example 27 (python):
```python
adata_test.X.data[:30]
```

Example 28 (unknown):
```unknown
array([1.768611 , 1.9229858, 3.635446 , 1.3192275, 1.4049321, 1.8123279,
       1.6739427, 2.9703567, 3.3852873, 1.2617257, 2.8007214, 0.7237267,
       1.4759332, 3.1692483, 3.266629 , 3.2549186, 3.8324249, 2.7257555,
       3.126333 , 3.7325323, 3.785544 , 4.073427 , 4.067536 , 4.1232815,
       3.4213552, 3.0830379, 3.7987761, 1.0650452, 3.5462437, 0.8590813],
      dtype=float32)
```

Example 29 (python):
```python
adata = sc.read_h5ad(f'{peakmatrix_dir}/Foetal_Peaks_tfidf.h5ad')
adata
```

Example 30 (unknown):
```unknown
AnnData object with n_obs × n_vars = 167022 × 508040
    obs: 'sangerID', 'combinedID', 'donor', 'facility', 'cell_or_nuclei', 'modality', 'kit_10x', 'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'HB_score', 'multiplexed', 'batch_key', 'region', 'FACSgate', 'sex', 'week', 'trimester', 'fine_grain', 'mid_grain', 'coarse_grain', 'heart_or_greatvessels', 'cycling', 'S_score', 'G2M_score', 'phase', 'stress_score', 'hb1_score'
```

Example 31 (python):
```python
# drop some obs columns
metadata_to_drop = [
       'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts',
       'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts',
       'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt',
       'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo',
       'pct_counts_ribo', 'HB_score', 'cycling','S_score','G2M_score','phase','stress_score','hb1_score']

adata.obs.drop(metadata_to_drop,axis=1,inplace=True)
```

Example 32 (python):
```python
# add peak metadata
meta = pd.read_csv('/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/peak_metadata.tsv',
           sep='\t')
meta.set_index('range',inplace=True)

# add to anndata
adata.var[meta.columns] = meta.reindex(adata.var_names)
adata.var.head()
```

Example 33 (python):
```python
# save
adata.write(f'{peakmatrix_dir}/Foetal_Peaks_tfidf.h5ad')
```

Example 34 (unknown):
```unknown
... storing 'seqnames' as categorical
... storing 'strand' as categorical
... storing 'GroupReplicate' as categorical
... storing 'nearestGene' as categorical
... storing 'peakType' as categorical
... storing 'nearestTSS' as categorical
```

Example 35 (python):
```python
adata.X.data[:30]
```

Example 36 (unknown):
```unknown
array([1.768611 , 1.9229858, 3.635446 , 1.3192275, 1.4049321, 1.8123279,
       1.6739427, 2.9703567, 3.3852873, 1.2617257, 2.8007214, 0.7237267,
       1.4759332, 3.1692483, 3.266629 , 3.2549186, 3.8324249, 2.7257555,
       3.126333 , 3.7325323, 3.785544 , 4.073427 , 4.067536 , 4.1232815,
       3.4213552, 3.0830379, 3.7987761, 1.0650452, 3.5462437, 0.8590813],
      dtype=float32)
```

Example 37 (unknown):
```unknown
f'{peakmatrix_dir}/Foetal_Peaks_tfidf.h5ad'
```

Example 38 (unknown):
```unknown
'/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/Foetal_Peaks_tfidf.h5ad'
```

Example 39 (unknown):
```unknown
# rclone to gdrive
rclone copy /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/Foetal_Peaks_tfidf.h5ad \
gdrive:JamesC_Kazumasa/Foetal_Heart/SanjayShinha/toSinhalab/anndata/Peak/
```

---

## Notebook

**URL:** http://127.0.0.1:9020/notebooks_html/Fig1_General_processing/ATAC/ATAC_preprocess/ArchR_no5-1_Project-to-Matrix_TFIDF.html

**Contents:**
- Read in peak matrix¶
- TF-IDF normalisation¶

Ref: https://www.archrproject.com/bookdown/creating-an-archrproject-1.html

Using Signac function ref: https://stuartlab.org/signac/reference/runtfidf

**Examples:**

Example 1 (unknown):
```unknown
library(ArchR)
library(tidyverse)
library(BSgenome.Hsapiens.UCSC.hg38)
library(SingleCellExperiment)
library(Signac)
```

Example 2 (python):
```python
/ |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    

ArchR : Version 1.0.2
For more information see our website : www.ArchRProject.com
If you encounter a bug please report : https://github.com/GreenleafLab/ArchR/issues

Loading Required Packages...

	Loading Package : grid v4.0.4

	Loading Package : gridExtra v2.3

	Loading Package : gtools v3.9.3

	Loading Package : gtable v0.3.0

	Loading Package : ggplot2 v3.4.0

	Loading Package : magrittr v2.0.3

	Loading Package : plyr v1.8.8

	Loading Package : stringr v1.4.0

	Loading Package : data.table v1.14.4

	Loading Package : matrixStats v0.62.0

	Loading Package : S4Vectors v0.28.1

	Loading Package : GenomicRanges v1.42.0

	Loading Package : BiocGenerics v0.36.1

	Loading Package : Matrix v1.3.2

	Loading Package : Rcpp v1.0.9

	Loading Package : SummarizedExperiment v1.20.0

	Loading Package : rhdf5 v2.34.0

Warning message in system("timedatectl", intern = TRUE):
“running command 'timedatectl' had status 1”
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ tibble  3.1.8      ✔ purrr   0.3.4 
✔ tidyr   1.2.1      ✔ dplyr   1.0.10
✔ readr   2.1.3      ✔ forcats 0.5.1 
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::arrange()         masks plyr::arrange()
✖ dplyr::between()         masks data.table::between()
✖ dplyr::collapse()        masks IRanges::collapse()
✖ dplyr::combine()         masks Biobase::combine(), BiocGenerics::combine(), gridExtra::combine()
✖ purrr::compact()         masks plyr::compact()
✖ dplyr::count()           masks matrixStats::count(), plyr::count()
✖ dplyr::desc()            masks IRanges::desc(), plyr::desc()
✖ tidyr::expand()          masks Matrix::expand(), S4Vectors::expand()
✖ tidyr::extract()         masks magrittr::extract()
✖ dplyr::failwith()        masks plyr::failwith()
✖ dplyr::filter()          masks stats::filter()
✖ dplyr::first()           masks S4Vectors::first(), data.table::first()
✖ dplyr::id()              masks plyr::id()
✖ dplyr::lag()             masks stats::lag()
✖ dplyr::last()            masks data.table::last()
✖ dplyr::mutate()          masks plyr::mutate()
✖ tidyr::pack()            masks Matrix::pack()
✖ BiocGenerics::Position() masks ggplot2::Position(), base::Position()
✖ purrr::reduce()          masks GenomicRanges::reduce(), IRanges::reduce()
✖ dplyr::rename()          masks S4Vectors::rename(), plyr::rename()
✖ purrr::set_names()       masks magrittr::set_names()
✖ dplyr::slice()           masks IRanges::slice()
✖ dplyr::summarise()       masks plyr::summarise()
✖ dplyr::summarize()       masks plyr::summarize()
✖ purrr::transpose()       masks data.table::transpose()
✖ tidyr::unpack()          masks Matrix::unpack()
Loading required package: BSgenome

Loading required package: Biostrings

Loading required package: XVector


Attaching package: ‘XVector’


The following object is masked from ‘package:purrr’:

    compact


The following object is masked from ‘package:plyr’:

    compact



Attaching package: ‘Biostrings’


The following object is masked from ‘package:base’:

    strsplit


Loading required package: rtracklayer

Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
```

Example 3 (unknown):
```unknown
# before starting a project we must set the ArchRGenome and default threads for parallelization.
# Setting default genome to Hg38.
addArchRGenome("hg38")
```

Example 4 (unknown):
```unknown
Setting default genome to Hg38.
```

Example 5 (unknown):
```unknown
# Setting default number of Parallel threads to 16
addArchRThreads(threads = 1)
```

Example 6 (unknown):
```unknown
Setting default number of Parallel threads to 1.
```

Example 7 (unknown):
```unknown
mat = readMM(file="/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/matrix.mtx.gz")
```

Example 8 (unknown):
```unknown
mat_norm = RunTFIDF(object = mat) # default scale factor is "scale.factor = 10000"
```

Example 9 (unknown):
```unknown
Performing TF-IDF normalization
```

Example 10 (unknown):
```unknown
dim(mat_norm)
```

Example 11 (unknown):
```unknown
mat_norm[1:10,1:10]
```

Example 12 (python):
```python
10 x 10 sparse Matrix of class "dgCMatrix"
                                                                            
 [1,] . . .        .        .        .         .        .        2.9902939 .
 [2,] . . .        .        .        .         .        .        .         .
 [3,] . . .        .        .        .         .        .        .         .
 [4,] . . .        .        .        .         .        .        .         .
 [5,] . . .        .        .        .         .        .        2.9349327 .
 [6,] . . 1.130476 1.087975 1.056641 0.7904304 1.256202 .        0.8824317 .
 [7,] . . .        .        .        .         .        .        .         .
 [8,] . . .        .        .        .         .        .        .         .
 [9,] . . 2.641712 .        .        .         .        2.138465 .         .
[10,] . . .        .        .        .         .        .        .         .
```

Example 13 (unknown):
```unknown
# save
writeMM(obj = mat_norm, file="/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/matrix_tfidf.mtx")
```

Example 14 (unknown):
```unknown
# at terminal
gzip -v /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/matrix_tfidf.mtx
```

---

## Notebook

**URL:** http://127.0.0.1:9020/notebooks_html/Fig1_General_processing/ATAC/ATAC_preprocess/ArchR_no3_peak-calling.html

**Contents:**
- Read in ArchR project¶
- Check cell number per sample¶
- Create one "Sample" label¶
- Create Pseudo-bulk Replicates¶
- Calling peaks¶
- Add Peak matrix¶
- Estract peakset as Granges object¶

Ref: https://www.archrproject.com/bookdown/creating-an-archrproject-1.html

**Examples:**

Example 1 (unknown):
```unknown
library(ArchR)
library(tidyverse)
library(BSgenome.Hsapiens.UCSC.hg38)
```

Example 2 (python):
```python
/ |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    

ArchR : Version 1.0.2
For more information see our website : www.ArchRProject.com
If you encounter a bug please report : https://github.com/GreenleafLab/ArchR/issues

Loading Required Packages...

	Loading Package : grid v4.0.4

	Loading Package : gridExtra v2.3

	Loading Package : gtools v3.9.3

	Loading Package : gtable v0.3.0

	Loading Package : ggplot2 v3.4.0

	Loading Package : magrittr v2.0.3

	Loading Package : plyr v1.8.8

	Loading Package : stringr v1.4.0

	Loading Package : data.table v1.14.4

	Loading Package : matrixStats v0.62.0

	Loading Package : S4Vectors v0.28.1

	Loading Package : GenomicRanges v1.42.0

	Loading Package : BiocGenerics v0.36.1

	Loading Package : Matrix v1.3.2

	Loading Package : Rcpp v1.0.9

	Loading Package : SummarizedExperiment v1.20.0

	Loading Package : rhdf5 v2.34.0

Warning message in system("timedatectl", intern = TRUE):
“running command 'timedatectl' had status 1”
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ tibble  3.1.8      ✔ purrr   0.3.4 
✔ tidyr   1.2.1      ✔ dplyr   1.0.10
✔ readr   2.1.3      ✔ forcats 0.5.1 
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::arrange()         masks plyr::arrange()
✖ dplyr::between()         masks data.table::between()
✖ dplyr::collapse()        masks IRanges::collapse()
✖ dplyr::combine()         masks Biobase::combine(), BiocGenerics::combine(), gridExtra::combine()
✖ purrr::compact()         masks plyr::compact()
✖ dplyr::count()           masks matrixStats::count(), plyr::count()
✖ dplyr::desc()            masks IRanges::desc(), plyr::desc()
✖ tidyr::expand()          masks Matrix::expand(), S4Vectors::expand()
✖ tidyr::extract()         masks magrittr::extract()
✖ dplyr::failwith()        masks plyr::failwith()
✖ dplyr::filter()          masks stats::filter()
✖ dplyr::first()           masks S4Vectors::first(), data.table::first()
✖ dplyr::id()              masks plyr::id()
✖ dplyr::lag()             masks stats::lag()
✖ dplyr::last()            masks data.table::last()
✖ dplyr::mutate()          masks plyr::mutate()
✖ tidyr::pack()            masks Matrix::pack()
✖ BiocGenerics::Position() masks ggplot2::Position(), base::Position()
✖ purrr::reduce()          masks GenomicRanges::reduce(), IRanges::reduce()
✖ dplyr::rename()          masks S4Vectors::rename(), plyr::rename()
✖ purrr::set_names()       masks magrittr::set_names()
✖ dplyr::slice()           masks IRanges::slice()
✖ dplyr::summarise()       masks plyr::summarise()
✖ dplyr::summarize()       masks plyr::summarize()
✖ purrr::transpose()       masks data.table::transpose()
✖ tidyr::unpack()          masks Matrix::unpack()
Loading required package: BSgenome

Loading required package: Biostrings

Loading required package: XVector


Attaching package: ‘XVector’


The following object is masked from ‘package:purrr’:

    compact


The following object is masked from ‘package:plyr’:

    compact



Attaching package: ‘Biostrings’


The following object is masked from ‘package:base’:

    strsplit


Loading required package: rtracklayer
```

Example 3 (unknown):
```unknown
setwd('/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR')
getwd()
```

Example 4 (unknown):
```unknown
# before starting a project we must set the ArchRGenome and default threads for parallelization.
# Setting default genome to Hg38.
addArchRGenome("hg38")
```

Example 5 (unknown):
```unknown
Setting default genome to Hg38.
```

Example 6 (unknown):
```unknown
# Setting default number of Parallel threads to 16
addArchRThreads(threads = 10)
```

Example 7 (unknown):
```unknown
Setting default number of Parallel threads to 10.
```

Example 8 (unknown):
```unknown
archr_project_path = '/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output'
proj = loadArchRProject(path = archr_project_path, showLogo = FALSE)
proj
```

Example 9 (unknown):
```unknown
Successfully loaded ArchRProject!


           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 10 (unknown):
```unknown
class: ArchRProject 
outputDirectory: /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output 
samples(37): BHF_F_Hea11064670_BHF_F_Hea11031823
  BHF_F_Hea11064671_BHF_F_Hea11031824 ...
  HCAHeartST13386009_HCAHeartST13303419
  HCAHeartST13386010_HCAHeartST13303420
sampleColData names(1): ArrowFiles
cellColData names(56): Sample TSSEnrichment ... hb1_score Clusters
numberOfCells(1): 167022
medianTSS(1): 11.614
medianFrags(1): 10338.5
```

Example 11 (unknown):
```unknown
# check
library(repr)
options(repr.plot.width=15, repr.plot.height=15)

cM <- confusionMatrix(paste0(proj$Sample), paste0(proj$fine_grain))
df = t(as.data.frame(as.matrix(cM)))
colnames(df) = c(1:ncol(df)) 
df
```

Example 12 (unknown):
```unknown
# check
library(repr)
options(repr.plot.width=15, repr.plot.height=15)

cM <- confusionMatrix(paste0(proj$Sample), paste0(proj$week))
df = t(as.data.frame(as.matrix(cM)))
colnames(df) = c(1:ncol(df)) 
df
```

Example 13 (unknown):
```unknown
library(repr)
options(repr.plot.width=15, repr.plot.height=15)

cM <- confusionMatrix(paste0(proj$fine_grain), paste0(proj$week))
df = t(as.data.frame(as.matrix(cM)))
# colnames(df) = c(1:ncol(df)) 
t(df)
```

Example 14 (unknown):
```unknown
proj$Sample2 = "1"
```

Example 15 (unknown):
```unknown
proj = addGroupCoverages(ArchRProj = proj, groupBy = "fine_grain", sampleLabels = "Sample2",
                        minReplicates = 3,
                        maxReplicates = 3,
                         minCells = 40,
                      maxCells = 500,
                        force = TRUE)
# maxReplicate = sample number
```

Example 16 (unknown):
```unknown
ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-ab73c00ce4-Date-2023-03-09_Time-18-45-28.log
If there is an issue, please report to github with logFile!

AtrialCardiomyocytesCycling (1 of 63) : CellGroups N = 2

AtrialCardiomyocytesLeft (2 of 63) : CellGroups N = 2

AtrialCardiomyocytesRight (3 of 63) : CellGroups N = 2

AtrioventricularNodeCardiomyocytes (4 of 63) : CellGroups N = 2

BCells (5 of 63) : CellGroups N = 2

BCellsMS4A1pos (6 of 63) : CellGroups N = 2

ChromaffinCells (7 of 63) : CellGroups N = 3

CoronaryArterialEndothelialCells (8 of 63) : CellGroups N = 2

CoronaryCapillaryEndothelialCells (9 of 63) : CellGroups N = 2

CoronaryPericytes (10 of 63) : CellGroups N = 2

CoronarySmoothMuscleCells (11 of 63) : CellGroups N = 2

CoronaryVenousEndothelialCells (12 of 63) : CellGroups N = 2

CoronaryVesselAdventitialFibroblasts (13 of 63) : CellGroups N = 2

DendriticCellsMature (14 of 63) : CellGroups N = 2

DendriticCellsType1 (15 of 63) : CellGroups N = 2

DuctusArteriosusSmoothMuscleCells (16 of 63) : CellGroups N = 2

EndocardialCells (17 of 63) : CellGroups N = 2

EndocardialCushionCells (18 of 63) : CellGroups N = 2

EpicardiumDerivedCells (19 of 63) : CellGroups N = 2

GreatVesselAdventitialFibroblasts (20 of 63) : CellGroups N = 2

GreatVesselArterialEndothelialCells (21 of 63) : CellGroups N = 2

GreatVesselSmoothMuscleCells (22 of 63) : CellGroups N = 2

GreatVesselVenousEndothelialCells (23 of 63) : CellGroups N = 2

InnateLymphoidCells (24 of 63) : CellGroups N = 2

LymphaticEndothelialCells (25 of 63) : CellGroups N = 2

LymphNodeFibroblasticReticularCells (26 of 63) : CellGroups N = 2

MacrophagesATF3pos (27 of 63) : CellGroups N = 2

MacrophagesCX3CR1pos (28 of 63) : CellGroups N = 2

MacrophagesLYVE1pos (29 of 63) : CellGroups N = 2

MacrophagesTIMD4pos (30 of 63) : CellGroups N = 2

MastCells (31 of 63) : CellGroups N = 2

Megakaryocytes (32 of 63) : CellGroups N = 3

MesothelialEpicardialCells (33 of 63) : CellGroups N = 2

MonocyteDerivedCells (34 of 63) : CellGroups N = 2

Monocytes (35 of 63) : CellGroups N = 3

MonocytesMPOpos (36 of 63) : CellGroups N = 3

MyocardialInterstitialFibroblasts1 (37 of 63) : CellGroups N = 2

MyocardialInterstitialFibroblasts2 (38 of 63) : CellGroups N = 2

Myofibroblasts (39 of 63) : CellGroups N = 2

NaturalKillerCells (40 of 63) : CellGroups N = 2

NeuronPrecursors (41 of 63) : CellGroups N = 2

ParaympatheticNeurons (42 of 63) : CellGroups N = 2

PericardialCells1 (43 of 63) : CellGroups N = 2

PericardialCells2 (44 of 63) : CellGroups N = 2

PericardialCells3 (45 of 63) : CellGroups N = 2

PlasmacytoidDendriticCells (46 of 63) : CellGroups N = 2

ProBCells (47 of 63) : CellGroups N = 2

SchwannCellPrecursors (48 of 63) : CellGroups N = 2

SchwannCells (49 of 63) : CellGroups N = 2

SinoatrialNodeCardiomyocytes (50 of 63) : CellGroups N = 2

SympatheticNeurons (51 of 63) : CellGroups N = 2

TCellsCD4pos (52 of 63) : CellGroups N = 2

TCellsCD8pos (53 of 63) : CellGroups N = 2

TregsCD4pos (54 of 63) : CellGroups N = 2

ValveEndothelialCells (55 of 63) : CellGroups N = 2

ValveInterstitialCells (56 of 63) : CellGroups N = 2

VentricularCardiomyocytesCycling (57 of 63) : CellGroups N = 2

VentricularCardiomyocytesLeftCompact (58 of 63) : CellGroups N = 2

VentricularCardiomyocytesLeftTrabeculated (59 of 63) : CellGroups N = 2

VentricularCardiomyocytesRightCompact (60 of 63) : CellGroups N = 2

VentricularCardiomyocytesRightTrabeculated (61 of 63) : CellGroups N = 2

VentricularConductionSystemDistal (62 of 63) : CellGroups N = 2

VentricularConductionSystemProximal (63 of 63) : CellGroups N = 2

2023-03-09 18:47:08 : Creating Coverage Files!, 1.658 mins elapsed.

2023-03-09 18:47:08 : Batch Execution w/ safelapply!, 1.658 mins elapsed.

2023-03-09 20:44:56 : Adding Kmer Bias to Coverage Files!, 119.458 mins elapsed.

Completed Kmer Bias Calculation

Adding Kmer Bias (1 of 130)

Adding Kmer Bias (2 of 130)

Adding Kmer Bias (3 of 130)

Adding Kmer Bias (4 of 130)

Adding Kmer Bias (5 of 130)

Adding Kmer Bias (6 of 130)

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Adding Kmer Bias (36 of 130)

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Adding Kmer Bias (38 of 130)

Adding Kmer Bias (39 of 130)

Adding Kmer Bias (40 of 130)

Adding Kmer Bias (41 of 130)

Adding Kmer Bias (42 of 130)

Adding Kmer Bias (43 of 130)

Adding Kmer Bias (44 of 130)

Adding Kmer Bias (45 of 130)

Adding Kmer Bias (46 of 130)

Adding Kmer Bias (47 of 130)

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Adding Kmer Bias (50 of 130)

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Adding Kmer Bias (55 of 130)

Adding Kmer Bias (56 of 130)

Adding Kmer Bias (57 of 130)

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Adding Kmer Bias (59 of 130)

Adding Kmer Bias (60 of 130)

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Adding Kmer Bias (62 of 130)

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Adding Kmer Bias (80 of 130)

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Adding Kmer Bias (83 of 130)

Adding Kmer Bias (84 of 130)

Adding Kmer Bias (85 of 130)

Adding Kmer Bias (86 of 130)

Adding Kmer Bias (87 of 130)

Adding Kmer Bias (88 of 130)

Adding Kmer Bias (89 of 130)

Adding Kmer Bias (90 of 130)

Adding Kmer Bias (91 of 130)

Adding Kmer Bias (92 of 130)

Adding Kmer Bias (93 of 130)

Adding Kmer Bias (94 of 130)

Adding Kmer Bias (95 of 130)

Adding Kmer Bias (96 of 130)

Adding Kmer Bias (97 of 130)

Adding Kmer Bias (98 of 130)

Adding Kmer Bias (99 of 130)

Adding Kmer Bias (100 of 130)

Adding Kmer Bias (101 of 130)

Adding Kmer Bias (102 of 130)

Adding Kmer Bias (103 of 130)

Adding Kmer Bias (104 of 130)

Adding Kmer Bias (105 of 130)

Adding Kmer Bias (106 of 130)

Adding Kmer Bias (107 of 130)

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Adding Kmer Bias (110 of 130)

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Adding Kmer Bias (116 of 130)

Adding Kmer Bias (117 of 130)

Adding Kmer Bias (118 of 130)

Adding Kmer Bias (119 of 130)

Adding Kmer Bias (120 of 130)

Adding Kmer Bias (121 of 130)

Adding Kmer Bias (122 of 130)

Adding Kmer Bias (123 of 130)

Adding Kmer Bias (124 of 130)

Adding Kmer Bias (125 of 130)

Adding Kmer Bias (126 of 130)

Adding Kmer Bias (127 of 130)

Adding Kmer Bias (128 of 130)

Adding Kmer Bias (129 of 130)

Adding Kmer Bias (130 of 130)

2023-03-09 20:54:24 : Finished Creation of Coverage Files!, 128.931 mins elapsed.

ArchR logging successful to : ArchRLogs/ArchR-addGroupCoverages-ab73c00ce4-Date-2023-03-09_Time-18-45-28.log
```

Example 17 (unknown):
```unknown
# need to make sure MACS2 is the latest version
pip install --upgrade --force-reinstall MACS2
```

Example 18 (unknown):
```unknown
?addReproduciblePeakSet
```

Example 19 (unknown):
```unknown
start_time <- Sys.time()

proj <- addReproduciblePeakSet(
    ArchRProj = proj, 
    groupBy = "fine_grain", 
    threads = 10,
    reproducibility = "2",
)

end_time <- Sys.time()
end_time - start_time
```

Example 20 (unknown):
```unknown
Searching For MACS2..

Found with $path!

ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-ab18b19e47-Date-2023-03-09_Time-20-54-24.log
If there is an issue, please report to github with logFile!

Calling Peaks with Macs2

2023-03-09 20:54:26 : Peak Calling Parameters!, 0.028 mins elapsed.
```

Example 21 (unknown):
```unknown
Group
AtrialCardiomyocytesCycling                               AtrialCardiomyocytesCycling
AtrialCardiomyocytesLeft                                     AtrialCardiomyocytesLeft
AtrialCardiomyocytesRight                                   AtrialCardiomyocytesRight
AtrioventricularNodeCardiomyocytes                 AtrioventricularNodeCardiomyocytes
BCells                                                                         BCells
BCellsMS4A1pos                                                         BCellsMS4A1pos
ChromaffinCells                                                       ChromaffinCells
CoronaryArterialEndothelialCells                     CoronaryArterialEndothelialCells
CoronaryCapillaryEndothelialCells                   CoronaryCapillaryEndothelialCells
CoronaryPericytes                                                   CoronaryPericytes
CoronarySmoothMuscleCells                                   CoronarySmoothMuscleCells
CoronaryVenousEndothelialCells                         CoronaryVenousEndothelialCells
CoronaryVesselAdventitialFibroblasts             CoronaryVesselAdventitialFibroblasts
DendriticCellsMature                                             DendriticCellsMature
DendriticCellsType1                                               DendriticCellsType1
DuctusArteriosusSmoothMuscleCells                   DuctusArteriosusSmoothMuscleCells
EndocardialCells                                                     EndocardialCells
EndocardialCushionCells                                       EndocardialCushionCells
EpicardiumDerivedCells                                         EpicardiumDerivedCells
GreatVesselAdventitialFibroblasts                   GreatVesselAdventitialFibroblasts
GreatVesselArterialEndothelialCells               GreatVesselArterialEndothelialCells
GreatVesselSmoothMuscleCells                             GreatVesselSmoothMuscleCells
GreatVesselVenousEndothelialCells                   GreatVesselVenousEndothelialCells
InnateLymphoidCells                                               InnateLymphoidCells
LymphaticEndothelialCells                                   LymphaticEndothelialCells
LymphNodeFibroblasticReticularCells               LymphNodeFibroblasticReticularCells
MacrophagesATF3pos                                                 MacrophagesATF3pos
MacrophagesCX3CR1pos                                             MacrophagesCX3CR1pos
MacrophagesLYVE1pos                                               MacrophagesLYVE1pos
MacrophagesTIMD4pos                                               MacrophagesTIMD4pos
MastCells                                                                   MastCells
Megakaryocytes                                                         Megakaryocytes
MesothelialEpicardialCells                                 MesothelialEpicardialCells
MonocyteDerivedCells                                             MonocyteDerivedCells
Monocytes                                                                   Monocytes
MonocytesMPOpos                                                       MonocytesMPOpos
MyocardialInterstitialFibroblasts1                 MyocardialInterstitialFibroblasts1
MyocardialInterstitialFibroblasts2                 MyocardialInterstitialFibroblasts2
Myofibroblasts                                                         Myofibroblasts
NaturalKillerCells                                                 NaturalKillerCells
NeuronPrecursors                                                     NeuronPrecursors
ParaympatheticNeurons                                           ParaympatheticNeurons
PericardialCells1                                                   PericardialCells1
PericardialCells2                                                   PericardialCells2
PericardialCells3                                                   PericardialCells3
PlasmacytoidDendriticCells                                 PlasmacytoidDendriticCells
ProBCells                                                                   ProBCells
SchwannCellPrecursors                                           SchwannCellPrecursors
SchwannCells                                                             SchwannCells
SinoatrialNodeCardiomyocytes                             SinoatrialNodeCardiomyocytes
SympatheticNeurons                                                 SympatheticNeurons
TCellsCD4pos                                                             TCellsCD4pos
TCellsCD8pos                                                             TCellsCD8pos
TregsCD4pos                                                               TregsCD4pos
ValveEndothelialCells                                           ValveEndothelialCells
ValveInterstitialCells                                         ValveInterstitialCells
VentricularCardiomyocytesCycling                     VentricularCardiomyocytesCycling
VentricularCardiomyocytesLeftCompact             VentricularCardiomyocytesLeftCompact
VentricularCardiomyocytesLeftTrabeculated   VentricularCardiomyocytesLeftTrabeculated
VentricularCardiomyocytesRightCompact           VentricularCardiomyocytesRightCompact
VentricularCardiomyocytesRightTrabeculated VentricularCardiomyocytesRightTrabeculated
VentricularConductionSystemDistal                   VentricularConductionSystemDistal
VentricularConductionSystemProximal               VentricularConductionSystemProximal
                                           nCells nCellsUsed nReplicates nMin
AtrialCardiomyocytesCycling                  1597        580           2   80
AtrialCardiomyocytesLeft                     4777        580           2   80
AtrialCardiomyocytesRight                    8187        580           2   80
AtrioventricularNodeCardiomyocytes            643        580           2   80
BCells                                       1369        580           2   80
BCellsMS4A1pos                               2559        580           2   80
ChromaffinCells                               112         84           3   40
CoronaryArterialEndothelialCells              353        353           2   80
CoronaryCapillaryEndothelialCells            2449        580           2   80
CoronaryPericytes                             688        580           2   80
CoronarySmoothMuscleCells                     415        415           2   80
CoronaryVenousEndothelialCells                539        539           2   80
CoronaryVesselAdventitialFibroblasts         1613        580           2   80
DendriticCellsMature                          156        156           2   76
DendriticCellsType1                           425        425           2   80
DuctusArteriosusSmoothMuscleCells            1159        580           2   80
EndocardialCells                             2690        580           2   80
EndocardialCushionCells                       224        224           2   80
EpicardiumDerivedCells                        340        340           2   80
GreatVesselAdventitialFibroblasts           31525        580           2   80
GreatVesselArterialEndothelialCells           929        580           2   80
GreatVesselSmoothMuscleCells                14126        580           2   80
GreatVesselVenousEndothelialCells             207        207           2   80
InnateLymphoidCells                           547        547           2   80
LymphaticEndothelialCells                    1282        580           2   80
LymphNodeFibroblasticReticularCells           969        580           2   80
MacrophagesATF3pos                            611        580           2   80
MacrophagesCX3CR1pos                          551        551           2   80
MacrophagesLYVE1pos                          4157        580           2   80
MacrophagesTIMD4pos                           303        303           2   80
MastCells                                     190        190           2   80
Megakaryocytes                                118         86           3   40
MesothelialEpicardialCells                   1214        580           2   80
MonocyteDerivedCells                          386        386           2   80
Monocytes                                     117         85           3   40
MonocytesMPOpos                                34         33           3   20
MyocardialInterstitialFibroblasts1           7671        580           2   80
MyocardialInterstitialFibroblasts2           5123        580           2   80
Myofibroblasts                               3214        580           2   80
NaturalKillerCells                           1406        580           2   80
NeuronPrecursors                              371        371           2   80
ParaympatheticNeurons                         264        264           2   80
PericardialCells1                            8967        580           2   80
PericardialCells2                             187        187           2   80
PericardialCells3                            1040        580           2   80
PlasmacytoidDendriticCells                    430        430           2   80
ProBCells                                     459        459           2   80
SchwannCellPrecursors                         759        580           2   80
SchwannCells                                 1166        580           2   80
SinoatrialNodeCardiomyocytes                  738        580           2   80
SympatheticNeurons                            354        354           2   80
TCellsCD4pos                                 4251        580           2   80
TCellsCD8pos                                 1810        580           2   80
TregsCD4pos                                  1461        580           2   80
ValveEndothelialCells                         186        186           2   80
ValveInterstitialCells                       2034        580           2   80
VentricularCardiomyocytesCycling             4977        580           2   80
VentricularCardiomyocytesLeftCompact        11397        580           2   80
VentricularCardiomyocytesLeftTrabeculated    5054        580           2   80
VentricularCardiomyocytesRightCompact       12008        580           2   80
VentricularCardiomyocytesRightTrabeculated   2269        580           2   80
VentricularConductionSystemDistal             531        531           2   80
VentricularConductionSystemProximal          1334        580           2   80
                                           nMax maxPeaks
AtrialCardiomyocytesCycling                 500   150000
AtrialCardiomyocytesLeft                    500   150000
AtrialCardiomyocytesRight                   500   150000
AtrioventricularNodeCardiomyocytes          500   150000
BCells                                      500   150000
BCellsMS4A1pos                              500   150000
ChromaffinCells                              40    42000
CoronaryArterialEndothelialCells            273   150000
CoronaryCapillaryEndothelialCells           500   150000
CoronaryPericytes                           500   150000
CoronarySmoothMuscleCells                   335   150000
CoronaryVenousEndothelialCells              459   150000
CoronaryVesselAdventitialFibroblasts        500   150000
DendriticCellsMature                         80    78000
DendriticCellsType1                         345   150000
DuctusArteriosusSmoothMuscleCells           500   150000
EndocardialCells                            500   150000
EndocardialCushionCells                     144   112000
EpicardiumDerivedCells                      260   150000
GreatVesselAdventitialFibroblasts           500   150000
GreatVesselArterialEndothelialCells         500   150000
GreatVesselSmoothMuscleCells                500   150000
GreatVesselVenousEndothelialCells           127   103500
InnateLymphoidCells                         467   150000
LymphaticEndothelialCells                   500   150000
LymphNodeFibroblasticReticularCells         500   150000
MacrophagesATF3pos                          500   150000
MacrophagesCX3CR1pos                        471   150000
MacrophagesLYVE1pos                         500   150000
MacrophagesTIMD4pos                         223   150000
MastCells                                   110    95000
Megakaryocytes                               40    43000
MesothelialEpicardialCells                  500   150000
MonocyteDerivedCells                        306   150000
Monocytes                                    40    42500
MonocytesMPOpos                              27    16500
MyocardialInterstitialFibroblasts1          500   150000
MyocardialInterstitialFibroblasts2          500   150000
Myofibroblasts                              500   150000
NaturalKillerCells                          500   150000
NeuronPrecursors                            291   150000
ParaympatheticNeurons                       184   132000
PericardialCells1                           500   150000
PericardialCells2                           107    93500
PericardialCells3                           500   150000
PlasmacytoidDendriticCells                  350   150000
ProBCells                                   379   150000
SchwannCellPrecursors                       500   150000
SchwannCells                                500   150000
SinoatrialNodeCardiomyocytes                500   150000
SympatheticNeurons                          274   150000
TCellsCD4pos                                500   150000
TCellsCD8pos                                500   150000
TregsCD4pos                                 500   150000
ValveEndothelialCells                       106    93000
ValveInterstitialCells                      500   150000
VentricularCardiomyocytesCycling            500   150000
VentricularCardiomyocytesLeftCompact        500   150000
VentricularCardiomyocytesLeftTrabeculated   500   150000
VentricularCardiomyocytesRightCompact       500   150000
VentricularCardiomyocytesRightTrabeculated  500   150000
VentricularConductionSystemDistal           451   150000
VentricularConductionSystemProximal         500   150000
```

Example 22 (unknown):
```unknown
2023-03-09 20:54:26 : Batching Peak Calls!, 0.028 mins elapsed.

2023-03-09 20:54:26 : Batch Execution w/ safelapply!, 0 mins elapsed.

2023-03-09 21:13:11 : Identifying Reproducible Peaks!, 18.778 mins elapsed.

2023-03-09 21:14:40 : Creating Union Peak Set!, 20.261 mins elapsed.

Converged after 14 iterations!

Plotting Ggplot!

2023-03-09 21:15:06 : Finished Creating Union Peak Set (508040)!, 20.694 mins elapsed.
```

Example 23 (unknown):
```unknown
Time difference of 20.703 mins
```

Example 24 (unknown):
```unknown
?addReproduciblePeakSet
```

Example 25 (unknown):
```unknown
proj = addPeakMatrix(proj)
```

Example 26 (unknown):
```unknown
ArchR logging to : ArchRLogs/ArchR-addPeakMatrix-ab40ab39a8-Date-2023-03-09_Time-21-15-06.log
If there is an issue, please report to github with logFile!

2023-03-09 21:15:07 : Batch Execution w/ safelapply!, 0 mins elapsed.

ArchR logging successful to : ArchRLogs/ArchR-addPeakMatrix-ab40ab39a8-Date-2023-03-09_Time-21-15-06.log
```

Example 27 (unknown):
```unknown
saveArchRProject(ArchRProj = proj, outputDirectory = "project_output", load = FALSE)
```

Example 28 (unknown):
```unknown
Saving ArchRProject...
```

Example 29 (unknown):
```unknown
PeakSet = getPeakSet(proj)
```

Example 30 (unknown):
```unknown
# cell number
n_cell = table(proj@cellColData$fine_grain)

# peak number
n_peak = sort(table(rownames(mcols(PeakSet))),decreasing = TRUE)
```

Example 31 (unknown):
```unknown
library(ggplot2)
library(ggrepel)

options(repr.plot.width=10, repr.plot.height=10)

df = data.frame(fine_grain=names(n_peak),
           n_peak=as.numeric(unname(n_peak)),
           n_cell=as.numeric(unname(n_cell[names(n_peak)])))
df = df[order(-df$n_peak),]

ggplot(df, aes(n_cell,n_peak)) +
  geom_point()
```

Example 32 (unknown):
```unknown
ggplot(df, aes(n_cell,n_peak)) +
  geom_point() +
  geom_text_repel(aes(label = fine_grain))
```

Example 33 (unknown):
```unknown
sessionInfo()
```

---

## Notebook

**URL:** http://127.0.0.1:9020/notebooks_html/Fig1_General_processing/ATAC/ATAC_preprocess/anndata_PeakMatrix_to_anndata.html

**Contents:**
- Read in¶
- Make anndata¶
- Add cell type annotation¶
- Refine metadata¶

ref: is peak matrix extracted with getMatrixFromProject normalized? NO https://github.com/GreenleafLab/ArchR/discussions/943

508040 rows × 0 columns

167022 rows × 0 columns

167022 rows × 0 columns

**Examples:**

Example 1 (python):
```python
import scanpy as sc
import pandas as pd
import numpy as np
import anndata

from scipy.io import mmwrite, mmread
from scipy.sparse import csr_matrix
```

Example 2 (unknown):
```unknown
!ls -l /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix
```

Example 3 (unknown):
```unknown
total 3673116
-rw-r--r-- 1 20383 1000624    1492397 Mar 12 20:40 barcodes.tsv.gz
-rw-r--r-- 1 20383 1000624    4082604 Mar 12 20:40 features.tsv.gz
-rw-r--r-- 1 20383 1000624 3755691976 Mar 12 20:40 matrix.mtx.gz
```

Example 4 (unknown):
```unknown
peakmatrix_dir = '/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix'
```

Example 5 (unknown):
```unknown
# peak matrix, not-binarised
mat = mmread(f'{peakmatrix_dir}/matrix.mtx.gz')
mat
```

Example 6 (python):
```python
<508040x167022 sparse matrix of type '<class 'numpy.int64'>'
	with 1173033588 stored elements in COOrdinate format>
```

Example 7 (python):
```python
# peak names
features = pd.read_csv(f'{peakmatrix_dir}/features.tsv.gz', header=None, sep='\t')[[0]]
features.set_index(0,inplace=True)
features
```

Example 8 (python):
```python
# cell barcodes
cells = pd.read_csv(f'{peakmatrix_dir}/barcodes.tsv.gz', header=None, sep='\t')[[1]]
cells.set_index(1,inplace=True)
cells
```

Example 9 (python):
```python
adata = anndata.AnnData(
    X=mat.T,
    obs=cells,
    var=features
)

# rename obs_names
adata.obs_names = [x.replace('#','_') for x in adata.obs_names]

# convert sparce matrix
adata.X = adata.X.tocsr()
adata.X
```

Example 10 (python):
```python
<167022x508040 sparse matrix of type '<class 'numpy.float32'>'
	with 1173033588 stored elements in Compressed Sparse Row format>
```

Example 11 (unknown):
```unknown
AnnData object with n_obs × n_vars = 167022 × 508040
```

Example 12 (python):
```python
adata.X.data[:10]
```

Example 13 (unknown):
```unknown
array([2., 2., 2., 2., 1., 1., 2., 1., 2., 2.], dtype=float32)
```

Example 14 (python):
```python
np.max(adata.X.data)
```

Example 15 (python):
```python
obs = pd.read_csv('/nfs/team205/heart/anndata_objects/Foetal/Feb28ObjectRaw.obs.csv',index_col=0)

# add cell type labels and other metadata
metadata_to_add = ['sangerID', 'combinedID', 'donor', 
       'facility', 'cell_or_nuclei', 'modality', 'kit_10x', 
       'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts',
       'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts',
       'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt',
       'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo',
       'pct_counts_ribo', 'HB_score', 'multiplexed',
        'batch_key','region','FACSgate','sex','week','trimester',
                     'fine_grain','mid_grain','coarse_grain',
                     'heart_or_greatvessels','cycling','S_score','G2M_score','phase','stress_score','hb1_score']
adata.obs[metadata_to_add] = obs[metadata_to_add].reindex(adata.obs_names).copy()
adata
```

Example 16 (unknown):
```unknown
AnnData object with n_obs × n_vars = 167022 × 508040
    obs: 'sangerID', 'combinedID', 'donor', 'facility', 'cell_or_nuclei', 'modality', 'kit_10x', 'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'HB_score', 'multiplexed', 'batch_key', 'region', 'FACSgate', 'sex', 'week', 'trimester', 'fine_grain', 'mid_grain', 'coarse_grain', 'heart_or_greatvessels', 'cycling', 'S_score', 'G2M_score', 'phase', 'stress_score', 'hb1_score'
```

Example 17 (python):
```python
adata.var.rename_axis('Peaks', axis=0, inplace=True)
```

Example 18 (python):
```python
# save
adata.write(f'{peakmatrix_dir}/Foetal_Peaks.h5ad')
```

Example 19 (unknown):
```unknown
... storing 'sangerID' as categorical
... storing 'combinedID' as categorical
... storing 'donor' as categorical
... storing 'facility' as categorical
... storing 'cell_or_nuclei' as categorical
... storing 'modality' as categorical
... storing 'kit_10x' as categorical
... storing 'multiplexed' as categorical
... storing 'batch_key' as categorical
... storing 'region' as categorical
... storing 'FACSgate' as categorical
... storing 'sex' as categorical
... storing 'week' as categorical
... storing 'trimester' as categorical
... storing 'fine_grain' as categorical
... storing 'mid_grain' as categorical
... storing 'coarse_grain' as categorical
... storing 'heart_or_greatvessels' as categorical
... storing 'cycling' as categorical
... storing 'phase' as categorical
```

Example 20 (python):
```python
adata = sc.read_h5ad(f'{peakmatrix_dir}/Foetal_Peaks.h5ad')
adata
```

Example 21 (unknown):
```unknown
AnnData object with n_obs × n_vars = 167022 × 508040
    obs: 'sangerID', 'combinedID', 'donor', 'facility', 'cell_or_nuclei', 'modality', 'kit_10x', 'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'HB_score', 'multiplexed', 'batch_key', 'region', 'FACSgate', 'sex', 'week', 'trimester', 'fine_grain', 'mid_grain', 'coarse_grain', 'heart_or_greatvessels', 'cycling', 'S_score', 'G2M_score', 'phase', 'stress_score', 'hb1_score'
```

Example 22 (python):
```python
# drop some obs columns
metadata_to_drop = [
       'scrublet_score', 'doublet_pval', 'doublet_bh_pval', 'n_genes', 'n_counts',
       'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts',
       'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt',
       'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo',
       'pct_counts_ribo', 'HB_score', 'cycling','S_score','G2M_score','phase','stress_score','hb1_score']

adata.obs.drop(metadata_to_drop,axis=1,inplace=True)
```

Example 23 (python):
```python
# add peak metadata
meta = pd.read_csv('/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/peak_metadata.tsv',
           sep='\t')
meta.set_index('range',inplace=True)

# add to anndata
adata.var[meta.columns] = meta.reindex(adata.var_names)
adata.var.head()
```

Example 24 (python):
```python
# save
adata.write(f'{peakmatrix_dir}/Foetal_Peaks.h5ad')
```

Example 25 (unknown):
```unknown
... storing 'seqnames' as categorical
... storing 'strand' as categorical
... storing 'GroupReplicate' as categorical
... storing 'nearestGene' as categorical
... storing 'peakType' as categorical
... storing 'nearestTSS' as categorical
```

Example 26 (python):
```python
adata.X.data[:30]
```

Example 27 (unknown):
```unknown
array([2., 2., 2., 2., 1., 1., 2., 1., 2., 2., 2., 2., 3., 1., 2., 2., 3.,
       1., 2., 2., 2., 2., 2., 2., 1., 1., 2., 4., 2., 2.], dtype=float32)
```

Example 28 (unknown):
```unknown
f'{peakmatrix_dir}/Foetal_Peaks.h5ad'
```

Example 29 (unknown):
```unknown
'/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/Foetal_Peaks.h5ad'
```

Example 30 (unknown):
```unknown
# rclone to gdrive
rclone copy /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/Foetal_Peaks.h5ad \
gdrive:JamesC_Kazumasa/Foetal_Heart/SanjayShinha/toSinhalab/anndata/Peak_foetal_global_raw.h5ad
```

Example 31 (python):
```python
adata.obs['cell_type3'].value_counts()
```

---

## Notebook

**URL:** http://127.0.0.1:9020/notebooks_html/Fig1_General_processing/ATAC/ATAC_preprocess/ArchR_no5-2_Project-to-Matrix.html

**Contents:**
- Read in ArchR project¶
- Peak matrix¶
- Save as matrix¶
- GeneScoreMatrix¶
- Save as matrix¶

Ref: https://www.archrproject.com/bookdown/creating-an-archrproject-1.html

**Examples:**

Example 1 (unknown):
```unknown
library(ArchR)
library(tidyverse)
library(BSgenome.Hsapiens.UCSC.hg38)
library(SingleCellExperiment)
```

Example 2 (python):
```python
/ |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    

ArchR : Version 1.0.2
For more information see our website : www.ArchRProject.com
If you encounter a bug please report : https://github.com/GreenleafLab/ArchR/issues

Loading Required Packages...

	Loading Package : grid v3.6.1

	Loading Package : gridExtra v2.3

	Loading Package : gtools v3.9.4

	Loading Package : gtable v0.3.3

	Loading Package : ggplot2 v3.4.2

	Loading Package : magrittr v2.0.3

	Loading Package : plyr v1.8.8

	Loading Package : stringr v1.5.0

	Loading Package : data.table v1.14.8

	Loading Package : matrixStats v1.0.0

	Loading Package : S4Vectors v0.24.4

	Loading Package : GenomicRanges v1.38.0

	Loading Package : BiocGenerics v0.32.0

	Loading Package : Matrix v1.5.4.1

	Loading Package : Rcpp v1.0.10

	Loading Package : SummarizedExperiment v1.16.1

	Loading Package : rhdf5 v2.30.1

── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.2     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ tibble    3.2.1
✔ lubridate 1.9.2     ✔ tidyr     1.3.0
✔ purrr     1.0.1     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ lubridate::%within%()    masks IRanges::%within%()
✖ dplyr::arrange()         masks plyr::arrange()
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✖ dplyr::desc()            masks IRanges::desc(), plyr::desc()
✖ tidyr::expand()          masks Matrix::expand(), S4Vectors::expand()
✖ tidyr::extract()         masks magrittr::extract()
✖ dplyr::failwith()        masks plyr::failwith()
✖ dplyr::filter()          masks stats::filter()
✖ dplyr::first()           masks S4Vectors::first(), data.table::first()
✖ lubridate::hour()        masks data.table::hour()
✖ dplyr::id()              masks plyr::id()
✖ lubridate::isoweek()     masks data.table::isoweek()
✖ dplyr::lag()             masks stats::lag()
✖ dplyr::last()            masks data.table::last()
✖ lubridate::mday()        masks data.table::mday()
✖ lubridate::minute()      masks data.table::minute()
✖ lubridate::month()       masks data.table::month()
✖ dplyr::mutate()          masks plyr::mutate()
✖ tidyr::pack()            masks Matrix::pack()
✖ BiocGenerics::Position() masks ggplot2::Position(), base::Position()
✖ lubridate::quarter()     masks data.table::quarter()
✖ purrr::reduce()          masks GenomicRanges::reduce(), IRanges::reduce()
✖ dplyr::rename()          masks S4Vectors::rename(), plyr::rename()
✖ lubridate::second()      masks S4Vectors::second(), data.table::second()
✖ lubridate::second<-()    masks S4Vectors::second<-()
✖ purrr::set_names()       masks magrittr::set_names()
✖ purrr::simplify()        masks DelayedArray::simplify()
✖ dplyr::slice()           masks IRanges::slice()
✖ dplyr::summarise()       masks plyr::summarise()
✖ dplyr::summarize()       masks plyr::summarize()
✖ purrr::transpose()       masks data.table::transpose()
✖ tidyr::unpack()          masks Matrix::unpack()
✖ lubridate::wday()        masks data.table::wday()
✖ lubridate::week()        masks data.table::week()
✖ lubridate::yday()        masks data.table::yday()
✖ lubridate::year()        masks data.table::year()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Loading required package: BSgenome

Loading required package: Biostrings

Loading required package: XVector


Attaching package: ‘XVector’


The following object is masked from ‘package:purrr’:

    compact


The following object is masked from ‘package:plyr’:

    compact



Attaching package: ‘Biostrings’


The following object is masked from ‘package:base’:

    strsplit


Loading required package: rtracklayer
```

Example 3 (unknown):
```unknown
# before starting a project we must set the ArchRGenome and default threads for parallelization.
# Setting default genome to Hg38.
addArchRGenome("hg38")
```

Example 4 (unknown):
```unknown
Setting default genome to Hg38.
```

Example 5 (unknown):
```unknown
# Setting default number of Parallel threads to 16
addArchRThreads(threads = 1)
```

Example 6 (unknown):
```unknown
Setting default number of Parallel threads to 1.
```

Example 7 (unknown):
```unknown
archr_project_path = '/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output'
proj = loadArchRProject(path = archr_project_path, showLogo = FALSE)
proj
```

Example 8 (unknown):
```unknown
Successfully loaded ArchRProject!


           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
```

Example 9 (unknown):
```unknown
class: ArchRProject 
outputDirectory: /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output 
samples(37): BHF_F_Hea11064670_BHF_F_Hea11031823
  BHF_F_Hea11064671_BHF_F_Hea11031824 ...
  HCAHeartST13386009_HCAHeartST13303419
  HCAHeartST13386010_HCAHeartST13303420
sampleColData names(1): ArrowFiles
cellColData names(63): Sample TSSEnrichment ... Gex_MitoRatio
  Gex_RiboRatio
numberOfCells(1): 167022
medianTSS(1): 11.614
medianFrags(1): 10338.5
```

Example 10 (unknown):
```unknown
PeakMatrix = getMatrixFromProject(
             ArchRProj = proj,
              useMatrix = "PeakMatrix",
              useSeqnames = NULL,
              verbose = TRUE,
              binarize = FALSE,
              threads = getArchRThreads(),
              logFile = createLogFile("getMatrixFromProject")
             )
```

Example 11 (unknown):
```unknown
ArchR logging to : ArchRLogs/ArchR-getMatrixFromProject-23502ed73aec-Date-2023-03-12_Time-19-51-39.log
If there is an issue, please report to github with logFile!

2023-03-12 20:13:14 : Organizing colData, 21.576 mins elapsed.

2023-03-12 20:13:16 : Organizing rowData, 21.621 mins elapsed.

2023-03-12 20:13:16 : Organizing rowRanges, 21.622 mins elapsed.

2023-03-12 20:13:16 : Organizing Assays (1 of 1), 21.624 mins elapsed.

2023-03-12 20:23:20 : Constructing SummarizedExperiment, 31.689 mins elapsed.

2023-03-12 20:29:42 : Finished Matrix Creation, 38.046 mins elapsed.
```

Example 12 (unknown):
```unknown
# get peak names as ranges
PeakSet = getPeakSet(proj)
df = data.frame(PeakSet)
ranges = paste0(df[['seqnames']],':',df[['start']],'_',df[['end']])
head(ranges)

# add rawnames of PeakMatrix
rownames(PeakMatrix) = ranges
PeakMatrix

# add rawnames of PeakMatrix binarised
# rownames(PeakMatrix_bi) = ranges
# PeakMatrix_bi
```

Example 13 (python):
```python
class: RangedSummarizedExperiment 
dim: 508040 167022 
metadata(0):
assays(1): PeakMatrix
rownames(508040): chr1:817093_817593 chr1:819818_820318 ...
  chrX:155881064_155881564 chrX:155881618_155882118
rowData names(1): idx
colnames(167022): 7089STDY13216921_BHF_F_Hea13242528#GCAATAGAGTTATGTG-1
  7089STDY13216921_BHF_F_Hea13242528#TGGGCCTAGATGGACA-1 ...
  BHF_F_Hea11933675_BHF_F_Hea11596628#GTACTAATCGTTTCCA-1
  7089STDY13216923_BHF_F_Hea13242530#GCTGGTTCAAATTCGT-1
colData names(63): BlacklistRatio Gex_MitoRatio ... ReadsInPeaks FRIP
```

Example 14 (unknown):
```unknown
# save as cell-by-peak
writeMM(obj = assay(PeakMatrix), file="/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/matrix.mtx")
```

Example 15 (unknown):
```unknown
write.table(rownames(PeakMatrix), file="/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/features.tsv",
           col.names = FALSE, row.names = FALSE, quote = FALSE, sep='\t')
```

Example 16 (unknown):
```unknown
# row.names = TRUE to put the features in the 2nd column (for scanpy.read_10x_mtx later we use)
write.table(colnames(PeakMatrix), file="/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/barcodes.tsv",
           col.names = FALSE, row.names = TRUE, quote = FALSE, sep='\t')
```

Example 17 (unknown):
```unknown
colnames(PeakMatrix)
```

Example 18 (unknown):
```unknown
# at farm
gzip -v /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/matrix.mtx
# gzip -v /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/matrix_binarised.mtx
gzip -v /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/features.tsv
gzip -v /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/PeakMatrix/barcodes.tsv
```

Example 19 (unknown):
```unknown
GeneScoreMatrix = getMatrixFromProject(
             ArchRProj = proj,
              useMatrix = "GeneScoreMatrix",
              useSeqnames = NULL,
              verbose = TRUE,
              binarize = FALSE,
              threads = getArchRThreads(),
              logFile = createLogFile("getMatrixFromProject")
             )
```

Example 20 (unknown):
```unknown
ArchR logging to : ArchRLogs/ArchR-getMatrixFromProject-2d21e6a568ca7-Date-2023-11-05_Time-22-34-07.log
If there is an issue, please report to github with logFile!

2023-11-05 23:01:34 : Organizing colData, 27.446 mins elapsed.

2023-11-05 23:01:38 : Organizing rowData, 27.515 mins elapsed.

2023-11-05 23:01:38 : Organizing rowRanges, 27.515 mins elapsed.

2023-11-05 23:01:38 : Organizing Assays (1 of 1), 27.516 mins elapsed.

2023-11-05 23:15:40 : Constructing SummarizedExperiment, 41.545 mins elapsed.

2023-11-05 23:15:45 : Finished Matrix Creation, 41.624 mins elapsed.
```

Example 21 (unknown):
```unknown
GeneScoreMatrix
```

Example 22 (python):
```python
class: SummarizedExperiment 
dim: 24919 167022 
metadata(0):
assays(1): GeneScoreMatrix
rownames: NULL
rowData names(6): seqnames start ... name idx
colnames(167022): 7089STDY13216921_BHF_F_Hea13242528#GCAATAGAGTTATGTG-1
  7089STDY13216921_BHF_F_Hea13242528#TGGGCCTAGATGGACA-1 ...
  BHF_F_Hea11933675_BHF_F_Hea11596628#GTACTAATCGTTTCCA-1
  7089STDY13216923_BHF_F_Hea13242530#GCTGGTTCAAATTCGT-1
colData names(63): BlacklistRatio Gex_MitoRatio ... ReadsInPeaks FRIP
```

Example 23 (unknown):
```unknown
length(colnames(GeneScoreMatrix))
head(colnames(GeneScoreMatrix))
```

Example 24 (unknown):
```unknown
# add rawnames of GeneScoreMatrix
rownames(GeneScoreMatrix) = rowData(GeneScoreMatrix)$name
GeneScoreMatrix
```

Example 25 (python):
```python
class: SummarizedExperiment 
dim: 24919 167022 
metadata(0):
assays(1): GeneScoreMatrix
rownames(24919): OR4F5 LOC729737 ... F8A2 TMLHE
rowData names(6): seqnames start ... name idx
colnames(167022): 7089STDY13216921_BHF_F_Hea13242528#GCAATAGAGTTATGTG-1
  7089STDY13216921_BHF_F_Hea13242528#TGGGCCTAGATGGACA-1 ...
  BHF_F_Hea11933675_BHF_F_Hea11596628#GTACTAATCGTTTCCA-1
  7089STDY13216923_BHF_F_Hea13242530#GCTGGTTCAAATTCGT-1
colData names(63): BlacklistRatio Gex_MitoRatio ... ReadsInPeaks FRIP
```

Example 26 (unknown):
```unknown
# save
writeMM(obj = assay(GeneScoreMatrix), file="/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/GeneScoreMatrix/matrix.mtx")
```

Example 27 (unknown):
```unknown
head(rownames(GeneScoreMatrix))
head(colnames(GeneScoreMatrix))
```

Example 28 (unknown):
```unknown
write.table(rownames(GeneScoreMatrix), file="/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/GeneScoreMatrix/features.tsv",
           col.names = FALSE, row.names = FALSE, quote = FALSE, sep='\t')

# row.names = TRUE to put the features in the 2nd column (for scanpy.read_10x_mtx later we use)
write.table(colnames(GeneScoreMatrix), file="/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/GeneScoreMatrix/barcodes.tsv",
           col.names = FALSE, row.names = TRUE, quote = FALSE, sep='\t')
```

Example 29 (unknown):
```unknown
%%bash
gzip -v /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/GeneScoreMatrix/matrix.mtx
gzip -v /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/GeneScoreMatrix/features.tsv
gzip -v /nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR/project_output/GeneScoreMatrix/barcodes.tsv
```

Example 30 (unknown):
```unknown
Error in parse(text = x, srcfile = src): <text>:1:1: unexpected input
1: %bash
    ^
Traceback:
```

---

## Notebook

**URL:** http://127.0.0.1:9020/notebooks_html/Fig1_General_processing/ATAC/ATAC_preprocess/ArchR_no1_createArrowFiles.html

**Contents:**
- Creat Arrow files¶

**Examples:**

Example 1 (unknown):
```unknown
library(ArchR)
library(tidyverse)
```

Example 2 (python):
```python
# Prepare input files
metadata = read.csv('/nfs/team205/heart/anndata_objects/Foetal/metadata/HeartTeamSamples_Mappeddata_20230208.csv')
metadata = metadata %>% filter(Publication=='Foetal')
metadata = metadata %>% filter(status=='Healthy')
metadata = metadata %>% filter(modality=='Multiome-ATAC')
nrow(metadata)

inputFiles = paste0(metadata %>% pull('Mapping_farm'),'/atac_fragments.tsv.gz')
names(inputFiles) = metadata %>% pull('CombinedID_Multiome')
inputFiles
```

Example 3 (unknown):
```unknown
# before starting a project we must set the ArchRGenome and default threads for parallelization.
# Setting default genome to Hg38.
addArchRGenome("hg38")
```

Example 4 (unknown):
```unknown
Setting default genome to Hg38.
```

Example 5 (unknown):
```unknown
# Setting default number of Parallel threads to 16
addArchRThreads(threads = 5)
```

Example 6 (unknown):
```unknown
Setting default number of Parallel threads to 5.
```

Example 7 (unknown):
```unknown
# ArrowFiles <- createArrowFiles(
#   inputFiles = inputFiles,
#   sampleNames = names(inputFiles),
#   minTSS = 4, #Dont set this too high because you can always increase later
#   minFrags = 1000, 
#   addTileMat = TRUE,
#   addGeneScoreMat = TRUE
# )
```

Example 8 (unknown):
```unknown
Using GeneAnnotation set by addArchRGenome(Hg38)!

Using GeneAnnotation set by addArchRGenome(Hg38)!

ArchR logging to : ArchRLogs/ArchR-createArrows-e075303579c-Date-2023-03-08_Time-01-11-16.log
If there is an issue, please report to github with logFile!

Cleaning Temporary Files

2023-03-08 01:11:17 : Batch Execution w/ safelapply!, 0 mins elapsed.
```

Example 9 (unknown):
```unknown
done_files = list.files('/nfs/team205/heart/anndata_objects/Foetal/multiome_ATAC/ArchR',pattern = '.arrow')
inputFiles_forrerun = inputFiles[setdiff(names(inputFiles),unlist(strsplit(done_files,'.arrow')))]
inputFiles_forrerun
```

Example 10 (unknown):
```unknown
ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles_forrerun,
  sampleNames = names(inputFiles_forrerun),
  minTSS = 4, #Dont set this too high because you can always increase later
  minFrags = 1000, 
  addTileMat = TRUE,
  addGeneScoreMat = TRUE
)
```

Example 11 (unknown):
```unknown
Using GeneAnnotation set by addArchRGenome(Hg38)!

Using GeneAnnotation set by addArchRGenome(Hg38)!

ArchR logging to : ArchRLogs/ArchR-createArrows-35a75076e3b-Date-2023-03-08_Time-18-21-49.log
If there is an issue, please report to github with logFile!

Cleaning Temporary Files

2023-03-08 18:21:50 : Batch Execution w/ safelapply!, 0 mins elapsed.

ArchR logging successful to : ArchRLogs/ArchR-createArrows-35a75076e3b-Date-2023-03-08_Time-18-21-49.log
```

Example 12 (unknown):
```unknown
?createArrowFiles
```

---
