pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
ena-database
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
geo-database
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
biomni
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
biopython
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
TF-differential-binding
The TF-differential-binding pipeline performs differential transcription factor (TF) binding analysis from ChIP-seq datasets (TF peaks) using the DiffBind package in R. It identifies genomic regions where TF binding intensity significantly differs between experimental conditions (e.g., treatment vs. control, mutant vs. wild-type). Use the TF-differential-binding pipeline when you need to analyze the different function of the same TF across two or more biological conditions, cell types, or treatments using ChIP-seq data or TF binding peaks. This pipeline is ideal for studying regulatory mechanisms that underlie transcriptional differences or epigenetic responses to perturbations.
motif-scanning
This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or ATAC-seq peaks. It utilizes HOMER to search for specific sequence motifs defined by position-specific scoring matrices (PSSMs) from known motif databases. Use this skill when you need to detect the presence and precise genomic coordinates of known TF binding motifs within experimentally defined regions such as ChIP-seq or ATAC-seq peaks.
UMR-LMR-PMD-detection
This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated Domains (PMDs) using whole-genome bisulfite sequencing (WGBS) methylation calls. The pipeline provides high-resolution enhancer-like LMRs, promoter-associated UMRs, and large-scale PMDs characteristic of reprogramming, aging, or cancer methylomes, enabling integration with chromatin accessibility, TF binding, and genome architecture analyses.
differential-tad-analysis
This skill performs differential topologically associating domain (TAD) analysis using HiCExplorer's hicDifferentialTAD tool. It compares Hi-C contact matrices between two conditions based on existing TAD definitions to identify significantly altered chromatin domains.
genomic-feature-annotation
This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information using Homer (Hypergeometric Optimization of Motif EnRichment). It annotates regions such as promoters, exons, introns, intergenic regions, and TSS proximity, and generates visual summaries of feature distributions.
hic-compartment-shift
This skill performs A/B compartment shift analysis between two Hi-C samples.
hic-loop-calling
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
local-methylation-profile
This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CTCF peak or other target regions).
known-motif-enrichment
This skill should be used when users need to perform known motif enrichment analysis on ChIP-seq, ATAC-seq, or other genomic peak files using HOMER (Hypergeometric Optimization of Motif EnRichment). It identifies enrichment of known transcription factor binding motifs from established databases in genomic regions.
beads
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pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
opentargets-database
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
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