Repositories list

• genepattern-server

  Public
  The GenePattern Server web application

  bioinformaticsgenomicsreproducible-research+ 1genepattern

  HTML

  •

  Other

  •17•36•0•4•Updated Dec 18, 2024Dec 18, 2024

• spatialGE.STenrich

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

  R

  •

  Other

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• 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

• spatialGE.STgradient

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

  R

  •

  Other

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• spatialGE.Preprocessing

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

  R

  •

  Other

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• spatialGE.STgradient.Launcher

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

  JavaScript

  •

  Other

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• Seurat.Preprocessing

  Public
  Seurat preprocessing module, part of the Seurat Suite.

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

• tfsites.FindTfSitesAlteredBySequenceVariation

  Public
  Farley Lab UCSD Collaboration

  Shell

  •

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

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

• tfsites.VisualizeTFSitesOnSequences

  Public
  Farley lab collaboration

  Other

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

• tfsites.NormalizeTfDNAAffinityData

  Public
  Farley lab UCSD collaboration

  Other

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

• common_module_code

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

  Other

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

• AuDIT

  Public
  AuDIT module

  R

  •

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

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

• spatialGE.STclust

  Public
  SpatialGE STClust module.

  R

  •

  Other

  •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

• tfsites.common_docker

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

  Dockerfile

  •

  Other

  •0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• spatialGE.STdiff

  Public
  STDiff function

  0•0•0•0•Updated Nov 6, 2024Nov 6, 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

• tfsites.AffinityScan

  Public
  Step 6 of tfsites workflow, as a GenePattern module

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

  •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

• tfsites.AnalyzeGenomeMPRA

  Public
  AnalyzeGWAS

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

  •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• tfsites.AnalyzeDifferentialBinding

  Public
  tfsites.DifferentialBindingAnalysis.py compares the e-scores between two PBM datasets.

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

  •0•0•0•0•Updated Jun 17, 2024Jun 17, 2024

• tfsites.IntegrateGenomeAnnotations

  Public
  tfsites.IntegrateGenomeAnnotations finds all possible SNVs and their effects on binding sites.

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

  •0•0•0•0•Updated Jun 17, 2024Jun 17, 2024

• tfsites.LoadGenome

  Public
  converts fasta file into dictionary and stores it as a pickled file.

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

  •0•0•0•0•Updated Jun 14, 2024Jun 14, 2024

• Harmony

  Public
  Wrapper Script for Harmony designed to work with GenePattern Module Integrator

  R

  •

  Other

  •0•0•0•0•Updated May 29, 2024May 29, 2024

• FcsToCsv

  Public
  Converts a Flow Cytometry Standard (FCS) file to a Comma Separated Values (CSV) file.

  0•0•0•0•Updated Apr 24, 2024Apr 24, 2024