Repositories list

• spatialGE.STgradient

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

  Other

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• spatialGE.STclust

  Public
  SpatialGE STClust module.

  R

  •

  Other

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• spatialGE.Preprocessing

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

  R

  •

  Other

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• genepattern-server

  Public
  The GenePattern Server web application

  bioinformaticsgenomicsreproducible-research+ 1genepattern

  HTML

  •

  Other

  •17•35•0•4•Updated Nov 12, 2024Nov 12, 2024

• spatialGE.STdiff

  Public
  STDiff function

  0•0•0•0•Updated Nov 6, 2024Nov 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 Oct 28, 2024Oct 28, 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 Oct 24, 2024Oct 24, 2024

• common_module_code

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

  Other

  •0•0•0•0•Updated Oct 21, 2024Oct 21, 2024

• tfsites.AnnotateAndVisualizeInSilicoSNVAnalysis

  Public
  Farley Lab UCSD Collaboration

  Shell

  •

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

  •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

• tfsites.AnnotateAndVisualizeTFSites

  Public
  Farley lab collaboration

  Other

  •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

• spatialGE.STenrich

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

  R

  •

  Other

  •0•0•0•0•Updated Sep 6, 2024Sep 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.defineTFBindingSitesFromPFM

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

  Shell

  •

  Other

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

• tfsites.DefineTfBindingSitesFromPBM

  Public
  Farley lab UCSD collaboration

  Other

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

• tfsites.common_docker

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

  Python

  •

  Other

  •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

• RandomForest.GPU

  Public
  Random Forest GPU, GenePattern - Mesirov Lab, UCSD

  random-forestgpuprediction+ 1random-forest-classifier

  Python

  •

  Other

  •0•1•2•0•Updated Mar 8, 2024Mar 8, 2024

• tximport.DESeq2

  Public
  tximport.DESeq2 wrapper module for GenePattern.

  R

  •1•0•0•0•Updated Mar 4, 2024Mar 4, 2024

• RandomForest

  Public
  Random Forest, GenePattern - Mesirov Lab, UCSD

  random-forestpredictionrandom-forest-classifier

  Python

  •

  Other

  •0•2•0•0•Updated Feb 28, 2024Feb 28, 2024

• Seurat.InteractiveUMAPVisualizer

  Public
  Seurat Interactive UMAP Visualizer developed by Julia Kononova. Made into Genepattern module by Edwin Huang, powered by Huggingface AI

  Jupyter Notebook

  •0•0•0•0•Updated Feb 26, 2024Feb 26, 2024

• tfsites.VisualizePhenotypicGenotypes

  Public
  Creates a visualization showing all SNV effects that overlap with genotypes

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

  •0•0•0•0•Updated Feb 16, 2024Feb 16, 2024

• tfsites.AnalyzeEQTLs

  Public
  Finds all effects of SNVs from GWAS data

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

  •0•0•0•0•Updated Feb 15, 2024Feb 15, 2024