Projects in Awesome Lists tagged with genepattern-module
A curated list of projects in awesome lists tagged with genepattern-module .
https://github.com/genepattern/dapple
Disease Association Protein-Protein Link Evaluator (Broad hosted algorithm)
community genepattern-module gparc user-contri
Last synced: 14 Apr 2025
https://github.com/genepattern/gistic_2.0
Genomic Identification of Significant Targets in Cancer
genepattern-module snp-analysis
Last synced: 25 Jan 2026
https://github.com/genepattern/examplemodule
This is basic GenePattern module written in Python 3. It can be taken as a Template for future modules. (click 'Use this template' to get started)
administration genepattern-module templates
Last synced: 10 Oct 2025
https://github.com/genepattern/hierarchicalclustering
GenePattern Hierarchical Clustering module.
Last synced: 20 Feb 2026
https://github.com/genepattern/stream.plot2dvisualization
UMap or TSNE validation plots
genepattern-module rna-seq single-cell
Last synced: 08 Jul 2025
https://github.com/genepattern/stream.detectleafgenes
Detect marker genes that distinguish the different trajectories
genepattern-module rna-seq single-cell
Last synced: 14 Sep 2025
https://github.com/genepattern/discover
GenePattern Module which implements the DiSCoVER algorithm
drug-repurposing genepattern-module prediction rna-seq
Last synced: 19 Mar 2026
https://github.com/genepattern/stream.visualizetrajectories
Generate the signature subway and stream plots
genepattern-module rna-seq single-cell
Last synced: 09 Aug 2025
https://github.com/genepattern/clsfilecreator
This a GenePattern Javascript visualizer that creates a CLS file from a GCT file.
Last synced: 19 Aug 2025
https://github.com/genepattern/stream.seedepgstructure
genepattern-module rna-seq single-cell
Last synced: 20 Feb 2026
https://github.com/genepattern/combat_seq
Batch effect adjustment based on negative binomial regression for RNA sequencing count data. Credits: https://github.com/zhangyuqing/ComBat-seq
batch-effects genepattern-module negative-binomial-regression rna-seq
Last synced: 20 Feb 2026
https://github.com/genepattern/stream.preprocess
Step one of the STREAM ssRNA-Seq Trajectory pipeline
genepattern-module rna-seq single-cell
Last synced: 20 Feb 2026
https://github.com/genepattern/stream.detectdifferentiallyexpressedgenes
Detect differentially expressed genes between pairs of trajectory branches
genepattern-module rna-seq single-cell
Last synced: 20 Feb 2026
https://github.com/genepattern/opencravat
OpenCRAVAT as a GenePattern module
genepattern-module variant-annotation
Last synced: 20 Feb 2026
https://github.com/genepattern/deseq2toodf
This module will turn a TXT file into ComparativeMarkerSelectionViewer-compatible ODF file
conversion genepattern-module utilities
Last synced: 20 Feb 2026
https://github.com/genepattern/stream.epgadjustfinalgraph
An optional final step to optimize branching, prune the graph or extend leaf nodes following generation of the Elastic Principal Graph
genepattern-module rna-seq single-cell
Last synced: 20 Feb 2026
https://github.com/genepattern/tcga.sampleselection
TCGA.SampleSelection wrapper module for GenePattern.
genepattern-module msigdb preprocess tcga utilities
Last synced: 20 Feb 2026
https://github.com/genepattern/heatmapviewer
A configurable heat map viewer that provides users with several options for manipulating and visualizing array-based data
Last synced: 20 Feb 2026
https://github.com/genepattern/kallisto.quant
GenePattern Notebook running Kallisto
genepattern-module kallisto pseudoalignment rna-seq rna-seq-analysis
Last synced: 20 Feb 2026
https://github.com/genepattern/stream.dimensionreduction
genepattern-module rna-seq single-cell
Last synced: 20 Feb 2026
https://github.com/genepattern/esppredictor
Determine which tryptic peptides will generate the highest signal in ESI-MS
Last synced: 20 Feb 2026
https://github.com/genepattern/hisat2.indexer
Repo for the HISAT2 .ndexer module which creates indices for the HISAT2.aligner module
bioinformatics genepattern-module rna-seq
Last synced: 20 Feb 2026
https://github.com/genepattern/stream.detectlabelspecificmarkers
STREAM can be used to detect cell population-specific markers. This is similar to leaf branch marker gene detection. Here instead of comparing the gene expression values between leaf branches, we compare the gene expression values between cell populations
genepattern-module rna-seq single-cell
Last synced: 20 Feb 2026
https://github.com/genepattern/affystexpressionfilecreator
Creates a GCT file from a set of CEL files from Affymetrix ST arrays.
affymetrix genepattern-module preprocess utility
Last synced: 20 Feb 2026
https://github.com/genepattern/conos.visualizegeneexpression
Visualize expression of genes of interest after Conos.Cluster has been ran.
genepattern-module single-cell singlecell
Last synced: 20 Feb 2026
https://github.com/genepattern/salmon.indexer
Salmon indexer wrapper module for GenePattern.
genepattern-module preprocess-and-utilities rna-seq
Last synced: 30 Jun 2025
https://github.com/genepattern/seurat.integratedata
GenePattern module which implements the batch correction algorithm within Seurat.
batch-correction data-integration genepattern-module seurat seurat-objects
Last synced: 20 Feb 2026
https://github.com/genepattern/stream.detecttransitiongenes
Detect transition genes for each branch of the trajectory.
genepattern-module rna-seq single-cell
Last synced: 20 Feb 2026
https://github.com/genepattern/hierarchicalclusteringviewer
Views results of hierarchical clustering.
Last synced: 19 Aug 2025
https://github.com/genepattern/stream.elasticprincipalgraph
Actual creation of the Elastic Principa Graph in the STREAM scRNASeq Trajectory analysis, packaged as a GenePattern module
genepattern-module rna-seq single-cell
Last synced: 20 Feb 2026
https://github.com/genepattern/mutpanning
Docker . module for the single cell toolkit
genepattern-module mutational-significance-analysis
Last synced: 03 Jul 2025
https://github.com/genepattern/comparativemarkerselection
Identify differentially expressed genes that can discriminate between distinct classes of samples.
differential-expression gene-list-selection genepattern-module
Last synced: 20 Feb 2026
https://github.com/genepattern/gsea2
Module for GSEA Julia Implementation
genepattern-module geneset-enrichment-analysis gsea julia
Last synced: 05 Oct 2025
https://github.com/genepattern/predictionresultsviewer
Visualizes prediction results
Last synced: 10 Oct 2025
https://github.com/genepattern/differentialexpressionviewer
Visualizes the results of ComparativeMarkerSelection
differential-expression genepattern-module javascript visualizer
Last synced: 11 Oct 2025
https://github.com/genepattern/cellfie
genepattern-module metabolomics pathway-analysis
Last synced: 15 Feb 2026
https://github.com/genepattern/stream.featureselection
genepattern-module rna-seq single-cell
Last synced: 10 Jul 2025
https://github.com/genepattern/htseq.count
HTSeq (0.11.2) wrapper module: Counting reads in features with 'htseq-count'
Last synced: 25 Jan 2026
https://github.com/genepattern/hisat2.aligner
Repo for the dockerized HISAT2.aligner module
bioinformatics genepattern-module rna-seq
Last synced: 12 Jul 2025
https://github.com/genepattern/geoimporter
Imports data from the Gene Expression Omnibus (GEO)
genepattern-module preprocess utility
Last synced: 19 Jul 2025