Skip to content

@genepattern GenePattern

Change the repository type filter

All

    Repositories list

    268 repositories

    • local_genepattern_runner_mcp

      Public
      Python
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • edgeR

      Public
      Python
      •
      Other
      •0•0•0•1•Updated Apr 22, 2026Apr 22, 2026

    • genepattern-server

      Public
      The GenePattern Server web application
      bioinformaticsgenomicsreproducible-research
      bioinformaticsgenomicsreproducible-researchgenepattern
      HTML
      •
      Other
      •19•37•0•4•Updated Apr 17, 2026Apr 17, 2026

    • common_module_code

      Public
      This repository contains the shared code used by the GenePattern modules.
      Other
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • module-toolkit

      Public
      Multi-agent AI pipeline that turns any bioinformatics CLI tool into a production-ready GenePattern module.
      pythonbioinformaticsgenomics
      pythonbioinformaticsgenomicsreproducible-researchmulti-agentscientific-computingcode-generationucsdworkflow-automationgenepattern
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•1•0•Updated Apr 15, 2026Apr 15, 2026

    • tfsites.CompareAcrossSeqsFromGenomicVariants

      Public
      Compares the two seqs and reports the binding site effect on diff seqs
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • tfsites.CompareAcrossSeqsFromDNA

      Public
      Compares the two seqs and reports the binding site effect on diff seqs
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • tfsites.PerturbTfSiteWithoutSideEffects

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • tfsites.FindTfSitesAlteredBySequenceVariation

      Public
      Farley Lab UCSD Collaboration
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • tfsites.VisualizeTFSitesOnSequences

      Public
      Farley lab collaboration
      Other
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • tfsites.GenerateMotifDatabase

      Public
      tfsites modules for defineBindingStites starting with Position Frequency Matrix from JASPAR
      Shell
      •
      Other
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • tfsites.NormalizeTfDNAAffinityData

      Public
      Farley lab UCSD collaboration
      Other
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • tfsites.common_docker

      Public
      Docker container for all the Farley lab tfsites suite of modules
      Shell
      •
      Other
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • gatk.SelectVariants

      Public
      Selects a subset of variants from a VCF file based on criteria such as variant type (SNP, INDEL), sample identity, JEXL filter expressions, and filtering status…
      Shell
      •0•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • gatk.Mutect2

      Public
      This is a python based tool used to call and run GATK Mutect2 in Genepattern
      Shell
      •2•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • CellTypist

      Public
      Python
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • piscem.indexer

      Public
      Python
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • MultiQC

      Public
      MultiQC is a tool to create a single interactive HTML report aggregating quality control metrics from multiple bioinformatics analyses across many samples.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • gatk.LearnReadOrientationModel

      Public
      Learns read orientation artifact priors from F1R2 counts produced by Mutect2 or CollectF1R2Counts. Uses an Expectation-Maximization algorithm to model orientati…
      Shell
      •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • gatk.FilterMutectCalls

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • gatk.GetPileupSummaries

      Public
      gatk GetPipelineSummaries as a GenePattern module
      Shell
      •
      Other
      •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • gatk.CalculateContamination

      Public
      "Given pileup data from GetPileupSummaries, calculates the fraction of reads coming from cross-sample contamination.
      Python
      •
      Other
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • genepattern-mcp

      Public
      MCP server that lets AI assistants (Claude, Cursor, Copilot) run GenePattern bioinformatics modules, manage cloud jobs, and access genomic data — all through na…
      pythondockerbioinformatics
      pythondockerbioinformaticsaigenomicsreproducible-researchmcpgene-expressionsingle-cellucsd
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Mar 25, 2026Mar 25, 2026

    • copilot

      Public
      Conversational AI for genomic science — ask questions in plain English, get expert-level bioinformatic answers.
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • genepattern-website

      Public
      GenePattern website and associated scripts
      HTML
      •0•0•0•0•Updated Jan 6, 2026Jan 6, 2026

    • AmpliconSuite

      Public
      Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.
      bioinformaticscancercopynumber
      bioinformaticscancercopynumbergenepattern-moduleecdna
      Python
      •
      Other
      •1•1•0•0•Updated Dec 5, 2025Dec 5, 2025

    • docker-aws-common-scripts

      Public
      common scripts for docker/aws batch containers used for GenePattern modules
      Shell
      •0•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • GeneListSignificanceViewer

      Public
      javascript rewrite of the GeneListSignificanceViewer for viewing marker results
      JavaScript
      •
      Other
      •0•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • Single.Cell.ssGSEA

      Public
      A version of Single Sample GSEA adapted to the sparsity of single cell RNA-seq data
      genepatterngseassgsea
      genepatterngseassgseagp-modulescgsea
      Python
      •
      Other
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • FeatureSummaryViewer

      Public
      js reimplementation of the FeatureSummaryViewer applet
      JavaScript
      •
      Other
      •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.