vep-variant-annotator
Variant Effect Predictor skill for comprehensive variant annotation with clinical database integration
tmb-msi-calculator
Tumor mutation burden and microsatellite instability calculation skill for immunotherapy biomarkers
ucsc-genome-browser-querier
UCSC Genome Browser query skill for genome annotation retrieval and track data access
acmg-variant-classifier
ACMG/AMP variant classification skill for systematic pathogenicity assessment
alphafold-predictor
AlphaFold protein structure prediction skill with confidence assessment and model analysis
autodock-docking-engine
AutoDock molecular docking skill for small molecule binding prediction and virtual screening
blast-sequence-search
BLAST skill for sequence similarity searching, homology detection, and database querying
bwa-aligner
BWA-MEM2 alignment skill for mapping sequencing reads to reference genomes with optimized parameter selection
cellranger-processor
Cell Ranger skill for 10X Genomics single-cell data processing
clinvar-querier
ClinVar database query skill for clinical variant interpretation and pathogenicity lookup
deepvariant-caller
DeepVariant deep learning variant calling skill for high-accuracy SNV and indel detection
deseq2-differential-expression
DESeq2 differential expression analysis skill with normalization, statistical modeling, and visualization
fastqc-quality-analyzer
Sequencing quality control skill for assessing read quality, adapter contamination, and sequence composition
fusion-gene-detector
Gene fusion detection skill for oncology applications with multiple caller integration
ga4gh-standards-validator
GA4GH standards compliance skill for data sharing and interoperability
gatk-variant-caller
GATK best practices skill for germline and somatic variant calling with joint genotyping
giab-benchmark-validator
Genome in a Bottle benchmark validation skill for pipeline accuracy assessment
gsea-pathway-analyzer
Gene Set Enrichment Analysis skill for functional annotation and pathway interpretation
hipaa-compliance-validator
HIPAA compliance validation skill for genomic data handling and audit
hpo-phenotype-matcher
Human Phenotype Ontology skill for phenotype-driven gene prioritization
humann-functional-profiler
HUMAnN functional profiling skill for metagenomic pathway analysis
igv-genome-browser
IGV integration skill for interactive genome visualization and review
kraken2-taxonomic-classifier
Kraken2 taxonomic classification skill for rapid metagenomic read assignment
mageck-crispr-analyzer
MAGeCK CRISPR screen analysis skill for gene essentiality scoring
maxquant-processor
MaxQuant mass spectrometry skill for protein identification and quantification
megahit-assembler
MEGAHIT metagenomic assembly skill for reconstructing genomes from short reads
metaphlan-profiler
MetaPhlAn metagenomic profiling skill for species-level community composition
nextflow-pipeline-executor
Nextflow workflow management skill for reproducible bioinformatics pipelines
perseus-statistical-analyzer
Perseus statistical analysis skill for proteomics data analysis and visualization
pharmgkb-annotator
PharmGKB pharmacogenomics annotation skill for drug-gene interaction assessment
phylogenetics-tree-builder
Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships
pymol-visualizer
PyMOL molecular visualization skill for structure rendering and analysis
qiime2-microbiome-analyzer
QIIME2 microbiome analysis skill for 16S rRNA profiling and diversity analysis
rdkit-chemoinformatics
RDKit chemoinformatics skill for molecular property calculation and compound library management
salmon-quantifier
Salmon pseudo-alignment skill for fast and accurate transcript quantification
samtools-bam-processor
BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data
seurat-single-cell-analyzer
Seurat single-cell analysis skill for clustering, annotation, and trajectory analysis
singularity-container-manager
Singularity container management skill for HPC-compatible containerized execution
snakemake-workflow-manager
Snakemake workflow management skill for rule-based pipeline execution
star-rnaseq-aligner
STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics
string-network-analyzer
STRING protein interaction network skill for functional enrichment and network visualization
structural-variant-detector
Structural variant detection skill for identifying CNVs, inversions, translocations, and complex rearrangements
dendrite-reforging-protocol
Reforge neural dendrite patterns after catastrophic failure.
go-db-query
Skills for querying Gene Ontology annotation databases in DuckDB format. Use this for queries about GO annotations, genes, terms, evidence codes, or taxonomic relationships in GO-DB databases (db/*.ddb files). Particularly useful for hierarchical queries using closure tables to find genes annotated to terms and their descendants.
