Skills tagged: genomics

• pysam - Python module for reading and writing genomic datasets

  bioinformaticsgenomicsngspysam

  ★ 0 · Updated 2026-09-21

  Reads, writes, and manipulates SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ genomic sequences using a Pythonic interface to htslib.

  ⚙ Read and write alignment files⚙ Perform pileup coverage analysis⚙ Read and write variant files
• validated-link-enrichment-analysis - Assess GCF-MF link predictions with Fisher exact test

  metabolomicsgenomicsenrichment analysisFisher exact test

  ★ 15 · Updated 2026-09-21

  Quantifies whether high-scoring GCF-MF link predictions are enriched for experimentally validated pairs using Fisher exact test.

  ⚙ Apply score percentile thresholds⚙ Calculate validated link proportions⚙ Perform Fisher exact test
• validated-link-proportional-comparison - Compare validated GCF-MF link enrichment across scores.

  metabolomicsgenomicsFisher exact testlink scoring

  ★ 15 · Updated 2026-09-21

  Compares enrichment of validated GCF-MF links across scoring categories using proportional analysis and Fisher exact tests.

  ⚙ Partition links into scoring categories⚙ Calculate validated link proportions⚙ Compute Fisher exact test p-values
• ensembl-database - Query Ensembl REST API for genomic data and variants

  ensemblgenomicsrest-apivariant-analysis

  ★ 586 · Updated 2026-09-19

  Query Ensembl genome database REST API for gene annotations, sequences, variant analysis, orthologs, and assembly coordinate mapping across species.

  ⚙ Retrieve gene annotations and information⚙ Retrieve DNA and protein sequences⚙ Analyze variant effect predictions
• bio-genome-intervals-coverage-analysis - Calculate depth and coverage across genomic intervals

  bedtoolsgenomecovcoveragebedgraph

  ★ 1 · Updated 2026-09-19

  Calculate read depth and coverage across genomic intervals using bedtools, generate bedGraph files, compute per-base depth, and summarize statistics.

  ⚙ Generate bedGraph files⚙ Compute per-base coverage depth⚙ Calculate feature coverage statistics
• ensembl-database - Query Ensembl database REST API for genomic research

  ensemblgenomicsbioinformaticsrest-api

  ★ 1 · Updated 2026-09-19

  Query gene annotations, sequences, variants, orthologs, VEP predictions, and assembly mappings across 250+ species via Ensembl REST API.

  ⚙ Retrieve gene information⚙ Fetch genomic sequences⚙ Analyze genetic variants
• ena-database - Query and retrieve data from European Nucleotide Archive

  genomicsbioinformaticsENAREST API

  ★ 17 · Updated 2026-09-19

  Access the European Nucleotide Archive via REST APIs and FTP or Aspera to search and retrieve sequences, raw reads, assemblies, and metadata.

  ⚙ Download raw sequencing reads⚙ Search records using metadata filters⚙ Retrieve record metadata
• bio-hi-c-analysis-compartment-analysis - Identify A/B compartments from Hi-C data with cooltools

  Hi-CA/B compartmentscooltoolschromatin structure

  ★ 1 · Updated 2026-09-19

  Detects A/B chromatin compartments from Hi-C contact matrices using cooltools eigenvector decomposition and quantifies compartmentalization strength.

  ⚙ Compute compartment eigenvectors⚙ Orient compartments using GC content⚙ Extract AB compartment calls
• ena-database - Access ENA nucleotide sequences and genomics metadata.

  genomicsbioinformaticsenanucleotide-sequence

  ★ 0 · Updated 2026-09-18

  Retrieves DNA/RNA sequences, raw FASTQ reads, genome assemblies, and metadata from the European Nucleotide Archive via REST APIs and FTP.

  ⚙ Retrieve nucleotide sequences and reads⚙ Search samples studies and assemblies⚙ Download FASTQ files and assemblies
• bio-epidemiological-genomics-transmission-inference - Infer pathogen transmission networks and transmission pairs

  epidemiologygenomicstransmission-inferencetransphylo

  ★ 0 · Updated 2026-09-18

  Infer pathogen transmission networks and estimate who-infected-whom from genomic and epidemiological data using TransPhylo and distance-based algorithms.

  ⚙ Infer transmission trees using TransPhylo⚙ Prepare input data for TransPhylo⚙ Extract consensus transmission tree
• bio-hi-c-analysis-tad-detection - Call TADs and boundary structures from Hi-C data

  hi-ctadcooltoolshicexplorer

  ★ 15 · Updated 2026-09-18

  Calls topologically associating domains (TADs) and domain boundaries from Hi-C contact matrices using insulation scores and HiCExplorer.

  ⚙ Compute Hi-C insulation scores⚙ Call TAD domain boundaries⚙ Extract TAD region intervals
• bio-hi-c-analysis-hic-data-io - Hi-C Data I/O and Matrix Manipulation

  hi-ccoolerhic2coolgenomics

  ★ 602 · Updated 2026-09-16

  Load, convert, access, merge, coarsen, and export Hi-C contact matrices using cooler and hic2cool.

  ⚙ Load cool and mcool files⚙ Access bin and pixel information⚙ Extract contact matrices and submatrices
• vdb - Guide user to query genomic datasets via labretriever MCP

  vdblabretrieverDuckDBgenomics

  ★ 2 · Updated 2026-09-15

  Orients users and guides effective query workflows for genomic datasets hosted on HuggingFace using labretriever DuckDB SQL MCP tools.

  ⚙ List registered view names⚙ Inspect dataset columns and types⚙ Retrieve column semantic roles
• gget - Genomic database queries and lookups with gget

  bioinformaticsgenomicsensemblblast

  ★ 0 · Updated 2026-09-14

  Query genomic databases, fetch sequences, run BLAST searches, and create evidence logs using the gget CLI or Python package.

  ⚙ Search Ensembl IDs and gene metadata⚙ Fetch nucleotide and amino acid sequences⚙ Run BLAST and BLAT lookups
• bio-variant-calling - Variant Calling with bcftools from BAM Alignments

  variant callingbcftoolsSNP detectionindel detection

  ★ 178 · Updated 2026-06-30

  Detect SNPs and indels from aligned reads using bcftools mpileup and call pipeline, generating VCF output from BAM files.

  ⚙ Call SNPs and indels from BAM⚙ Generate pileup from aligned reads⚙ Call variants for specific regions
• tooluniverse - Unified access to 600+ scientific research tools

  scientific toolsbioinformaticscheminformaticsdrug discovery

  ★ 18 · Updated 2026-06-30

  Provides standardized access to 600+ scientific tools across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery.

  ⚙ Discover scientific tools by search⚙ Execute scientific tools via protocol⚙ Compose multi-step research workflows
• tooluniverse - Scientific Research Tools and Workflows

  bioinformaticscheminformaticsgenomicsdrug discovery

  ★ 2 · Updated 2026-06-30

  Discover, execute, and compose 600+ scientific tools across bioinformatics, cheminformatics, genomics, and drug discovery domains.

  ⚙ discover scientific tools⚙ execute scientific tools⚙ compose multi-step workflows
• scvelo - RNA Velocity Analysis for Single-Cell Data

  single-cellRNA-seqtrajectory inferencebioinformatics

  ★ 5 · Updated 2026-06-30

  Estimate cell state transitions from unspliced/spliced mRNA dynamics in single-cell RNA-seq data

  ⚙ load data⚙ filter and normalize⚙ compute moments
• anndata - Manage AnnData Objects

  single-cell RNA-seqbioinformaticsgenomicsdata processing

  ★ 394 · Updated 2026-06-30

  Manage AnnData objects for single-cell genomics and biological datasets

  ⚙ create AnnData object⚙ read h5ad file⚙ write h5ad file
• anndata - Annotated Data Matrix Management for Python

  bioinformaticssingle-cellgenomicsdata-structure

  ★ 422 · Updated 2026-06-30

  Handle annotated data matrices with metadata in Python

  ⚙ create AnnData objects⚙ read h5ad files⚙ write h5ad files

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