There are no reviews yet. Be the first to send feedback to the community and the maintainers!
genepattern-notebook
Platform for integrating genomic analysis with Jupyter Notebooks.genepattern-server
The GenePattern Server web applicationgenepattern-python
GenePattern Python Librarysingle_cell_clustering_notebook
NearestTemplatePrediction
Nearest neighbor prediction based on a list of marker genesABSOLUTE
Contains gp-unit tests for ABSOLUTE modulesDAPPLE
Disease Association Protein-Protein Link Evaluator (Broad hosted algorithm)MergeHTSeqCounts
Merges individial files containing HTSeq read counts into one fileDESeq2
A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductornmf-gpu
GPU-optimized NMF and variationsSubMap
Maps subclasses between two data setsMutSigCV
Identifies genes that are significantly mutated in cancer genomes, using a model with mutational covariates.notebook-repository
Code used in the operation of the GenePattern Notebook RepositoryRandomForest
Random Forest, GenePattern - Mesirov Lab, UCSDdocker-mutsigcv
GenePattern container for MutSigCV module on docker and/or AWS BatchSeurat.scATAC-seq
Seurat scATAC-seq moduleVoomNormalize
RTutorialModule
A tutorial module for writing GenePattern modules in R.docker-cogaps
HierarchicalClustering
GenePattern Hierarchical Clustering module.Seurat.Preprocessing
Seurat preprocessing module, part of the Seurat Suite.FastQC
Provides quality control metrics on raw sequence data.docker-amaretto
Docker container and module wrapper for Amaretto from the Gavaert Lab at Stanford (http://med.stanford.edu/gevaertlab/software.html)Tangram
A method for mapping sc/snRNA-seq data to various forms of spatial data collected from the same region.RankNormalize
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)Trimmomatic
Provides a variety of options for trimming Illumina FASTQ files of adapter sequences and low-quality reads.gpnotebook-website
GenePattern Notebook Website (old)removeSamples
Remove samples in dataset (.gct), using a list of samples providedCummeRbund
STREAM.Plot2DVisualization
UMap or TSNE validation plotsmodule-devkit
GenePattern Module Development tools -- helper scripts for packaging and publishing modulesRandomForest.GPU
Random Forest GPU, GenePattern - Mesirov Lab, UCSDScanpyUtilities
Single-cell preprocessing (annotation and filtering) GenePattern module using ScanpyTCGAImporter
This module takes in a GDC manifest file, download the files listed on that manifest, and renames them to be human-friendly.docker-java17
docker-r-3-2
docker/aws batch container for R 3.2 GenePattern modulesLove Open Source and this site? Check out how you can help us