Repositories list

• Single.Cell.ssGSEA

  Public
  The method for this module is still under active development, not finalized, and should not be used.

  genepatterngseassgsea+ 2gp-modulescgsea

  Python

  •

  Other

  •0•0•0•0•Updated Mar 10, 2025Mar 10, 2025

• genepattern-website

  Public
  GenePattern website and associated scripts

  HTML

  •0•0•0•0•Updated Mar 8, 2025Mar 8, 2025

• spatialGE.STdiff

  Public
  STDiff function

  R

  •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• spatialGE.STclust

  Public
  SpatialGE STClust module.

  R

  •

  Other

  •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• CorrelationMatrix

  Public
  Correlation Matrix module

  Python

  •

  Other

  •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• genepattern-server

  Public
  The GenePattern Server web application

  bioinformaticsgenomicsreproducible-research+ 1genepattern

  HTML

  •

  Other

  •17•36•0•4•Updated Mar 5, 2025Mar 5, 2025

• h5adtoGCT

  Public
  h5adtoGCT tool

  Python

  •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

• common_module_code

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

  Other

  •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025

• tfsites.FindTfSitesAlteredBySequenceVariation

  Public
  Farley Lab UCSD Collaboration

  Shell

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025

• tfsites.VisualizeTFSitesOnSequences

  Public
  Farley lab collaboration

  Other

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• tfsites.common_docker

  Public
  Docker container for all the Farley lab tfsites suite of modules

  Dockerfile

  •

  Other

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• spatialGE.STgradient.Launcher

  Public
  Launch expression spatial gradients based on https://github.com/FridleyLab/spatialGE

  JavaScript

  •

  Other

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• spatialGE.STplot.Launcher

  Public
  JavaScript

  •

  Other

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• spatialGE.STgradient

  Public
  Expression spatial gradients based on https://github.com/FridleyLab/spatialGE

  R

  •

  Other

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• spatialGE.STenrich

  Public
  Spatial enrichment of gene sets based on https://github.com/FridleyLab/spatialGE

  R

  •

  Other

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• spatialGE.STplot

  Public
  R

  •

  Other

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• spatialGE.Preprocessing

  Public
  Repo for the GenePattern Preprocessing module based on https://github.com/FridleyLab/spatialGE

  R

  •

  Other

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• tfsites.MapTfDNAInteractions

  Public
  Maps the crystal structure for a transcription factor

  Python

  •

  Other

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• tfsites.NormalizeTfDNAAffinityData

  Public
  Farley lab UCSD collaboration

  Other

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• AuDIT

  Public
  AuDIT module

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• AmpliconSuite

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

  bioinformaticscancercopynumber+ 2genepattern-moduleecdna

  Python

  •

  Other

  •2•1•0•0•Updated Dec 17, 2024Dec 17, 2024

• Seurat.Preprocessing

  Public
  Seurat preprocessing module, part of the Seurat Suite.

  0•1•0•0•Updated Dec 12, 2024Dec 12, 2024

• tfsites.GenerateMotifDatabase

  Public
  tfsites modules for defineBindingStites starting with Position Frequency Matrix from JASPAR

  Shell

  •

  Other

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• spatialGE.SpatialAutocorrelation

  Public
  SpatialGE STHet and compare_SThet functions

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• lohhla

  Public
  lohhla mystery module

  R

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• Tangram

  Public
  A method for mapping sc/snRNA-seq data to various forms of spatial data collected from the same region.

  Python

  •0•1•0•0•Updated Dec 3, 2024Dec 3, 2024

• Tangram.GPU

  Public
  Python

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• AmpliconSuiteAggregator

  Public
  Aggregates the results from AmpliconSuite

  Python

  •

  Other

  •4•0•0•1•Updated Aug 19, 2024Aug 19, 2024

• Seurat.Clustering

  Public
  Clustering and diff expression for Seurat RDS files

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 12, 2024Aug 12, 2024

• genepattern-notebook

  Public
  Platform for integrating genomic analysis with Jupyter Notebooks.

  bioinformaticsreproducible-researchnbextension+ 3genepatternpythonjupyter

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •12•44•0•0•Updated Aug 6, 2024Aug 6, 2024