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GenePattern

A Platform for Reproducible Bioinformatics

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  1. genepattern-notebook genepattern-notebook Public

    Platform for integrating genomic analysis with Jupyter Notebooks.

    Python 44 13

  2. genepattern-server genepattern-server Public

    The GenePattern Server web application

    HTML 36 18

  3. genepattern-python genepattern-python Public

    GenePattern Python Library

    Python 11 4

Repositories

Showing 10 of 248 repositories
  • AmpliconSuite Public Forked from edwin5588/paa_custom

    Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.

    genepattern/AmpliconSuite’s past year of commit activity
    Python 1 2 0 0 Updated Apr 25, 2025
  • tfsites.common_docker Public

    Docker container for all the Farley lab tfsites suite of modules

    genepattern/tfsites.common_docker’s past year of commit activity
    Dockerfile 0 0 0 0 Updated Apr 17, 2025
  • tfsites.CompareTfSitesAcrossSequences Public

    Compares the two seqs and reports the binding site effect on diff seqs

    genepattern/tfsites.CompareTfSitesAcrossSequences’s past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Apr 16, 2025
  • tfsites.GenerateMotifDatabase Public

    tfsites modules for defineBindingStites starting with Position Frequency Matrix from JASPAR

    genepattern/tfsites.GenerateMotifDatabase’s past year of commit activity
    Shell 0 0 0 0 Updated Apr 9, 2025
  • common_module_code Public

    This repository contains the shared code used by the GenePattern modules.

    genepattern/common_module_code’s past year of commit activity
    0 0 0 0 Updated Apr 7, 2025
  • tfsites.FindTfSitesAlteredBySequenceVariation Public

    Farley Lab UCSD Collaboration

    genepattern/tfsites.FindTfSitesAlteredBySequenceVariation’s past year of commit activity
    Shell 0 BSD-3-Clause 0 0 0 Updated Apr 4, 2025
  • tfsites.NormalizeTfDNAAffinityData Public

    Farley lab UCSD collaboration

    genepattern/tfsites.NormalizeTfDNAAffinityData’s past year of commit activity
    0 0 0 0 Updated Apr 4, 2025
  • tfsites.VisualizeTFSitesOnSequences Public

    Farley lab collaboration

    genepattern/tfsites.VisualizeTFSitesOnSequences’s past year of commit activity
    0 0 0 0 Updated Apr 4, 2025
  • citation-stats Public

    Citation Stats in a module format

    genepattern/citation-stats’s past year of commit activity
    Python 0 0 0 0 Updated Apr 1, 2025
  • h5adtoGCT Public

    H5adToGCT is a Python-based tool that converts AnnData (h5ad) files to Gene Cluster Text (GCT) format. This tool is particularly useful for single-cell RNA-seq data analysis workflows.

    genepattern/h5adtoGCT’s past year of commit activity
    Python 0 0 0 0 Updated Apr 1, 2025
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