Pinned Repositories
ABSOLUTE
Contains gp-unit tests for ABSOLUTE modules
DAPPLE
Disease Association Protein-Protein Link Evaluator (Broad hosted algorithm)
DESeq2
A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor
genepattern-notebook
Platform for integrating genomic analysis with Jupyter Notebooks.
genepattern-python
GenePattern Python Library
genepattern-server
The GenePattern Server web application
MergeHTSeqCounts
Merges individial files containing HTSeq read counts into one file
NearestTemplatePrediction
Nearest neighbor prediction based on a list of marker genes
nmf-gpu
GPU-optimized NMF and variations
single_cell_clustering_notebook
GenePattern's Repositories
genepattern/genepattern-notebook
Platform for integrating genomic analysis with Jupyter Notebooks.
genepattern/genepattern-server
The GenePattern Server web application
genepattern/genepattern-python
GenePattern Python Library
genepattern/AmpliconSuiteAggregator
Aggregates the results from AmpliconSuite
genepattern/RandomForest
Random Forest, GenePattern - Mesirov Lab, UCSD
genepattern/AmpliconSuite
Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.
genepattern/ComBat
Performs batch correction on a dataset containing multiple batches
genepattern/RandomForest.GPU
Random Forest GPU, GenePattern - Mesirov Lab, UCSD
genepattern/Tangram
A method for mapping sc/snRNA-seq data to various forms of spatial data collected from the same region.
genepattern/common_module_code
This repository contains the shared code used by the GenePattern modules.
genepattern/Harmony
Wrapper Script for Harmony designed to work with GenePattern Module Integrator
genepattern/ComBat_Seq
Batch effect adjustment based on negative binomial regression for RNA sequencing count data. Credits: https://github.com/zhangyuqing/ComBat-seq
genepattern/FcsToCsv
Converts a Flow Cytometry Standard (FCS) file to a Comma Separated Values (CSV) file.
genepattern/nmf
Module for performing non-negative matrix factorization
genepattern/scVelo
scVelo wrapper module for GenePattern
genepattern/Seurat.InteractiveUMAPVisualizer
Seurat Interactive UMAP Visualizer developed by Julia Kononova. Made into Genepattern module by Edwin Huang, powered by Huggingface AI
genepattern/tfsites.AffinityScan
Step 6 of tfsites workflow, as a GenePattern module
genepattern/tfsites.AnalyzeEQTLs
Finds all effects of SNVs from GWAS data
genepattern/tfsites.AnalyzeGenomeMPRA
AnalyzeGWAS
genepattern/tfsites.AnnotateAndVisualizeInSilicoSNVAnalysis
Farley Lab UCSD Collaboration
genepattern/tfsites.AnnotateAndVisualizeTFSites
Farley lab collaboration
genepattern/tfsites.common_docker
Docker container for all the Farley lab tfsites suite of modules
genepattern/tfsites.CompareEnhancers
Compares the two seqs and reports the binding site effect on diff seqs
genepattern/tfsites.DefineTfBindingSitesFromPBM
Farley lab UCSD collaboration
genepattern/tfsites.defineTFBindingSitesFromPFM
tfsites modules for defineBindingStites starting with Position Frequency Matrix from JASPAR
genepattern/tfsites.DifferentialBindingAnalysis
tfsites.DifferentialBindingAnalysis.py compares the e-scores between two PBM datasets.
genepattern/tfsites.IntegrateGenomeAnnotations
tfsites.IntegrateGenomeAnnotations finds all possible SNVs and their effects on binding sites.
genepattern/tfsites.LoadGenome
converts fasta file into dictionary and stores it as a pickled file.
genepattern/tfsites.VisualizePhenotypicGenotypes
Creates a visualization showing all SNV effects that overlap with genotypes
genepattern/tximport.DESeq2
tximport.DESeq2 wrapper module for GenePattern.