genepattern/ScanpyUtilities

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genepattern/ScanpyUtilities

genepattern

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Single-cell preprocessing (annotation and filtering) GenePattern module using Scanpy

genepattern-notebook

Platform for integrating genomic analysis with Jupyter Notebooks.

genepattern-server

The GenePattern Server web application

genepattern-python

GenePattern Python Library

single_cell_clustering_notebook

Jupyter Notebook

NearestTemplatePrediction

Nearest neighbor prediction based on a list of marker genes

ABSOLUTE

Contains gp-unit tests for ABSOLUTE modules

DAPPLE

Disease Association Protein-Protein Link Evaluator (Broad hosted algorithm)

MergeHTSeqCounts

Merges individial files containing HTSeq read counts into one file

DESeq2

A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor

nmf-gpu

GPU-optimized NMF and variations

SubMap

Maps subclasses between two data sets

MutSigCV

Identifies genes that are significantly mutated in cancer genomes, using a model with mutational covariates.

GISTIC_2.0

Genomic Identification of Significant Targets in Cancer

notebook-repository

Code used in the operation of the GenePattern Notebook Repository

RandomForest

Random Forest, GenePattern - Mesirov Lab, UCSD

docker-mutsigcv

GenePattern container for MutSigCV module on docker and/or AWS Batch

Seurat.scATAC-seq

Seurat scATAC-seq module

VoomNormalize

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 provided

CummeRbund

STREAM.Plot2DVisualization

UMap or TSNE validation plots

module-devkit

GenePattern Module Development tools -- helper scripts for packaging and publishing modules

RandomForest.GPU

Random Forest GPU, GenePattern - Mesirov Lab, UCSD

TCGAImporter

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 modules