GenePattern

GenePattern's repositories

genepattern-notebook

Platform for integrating genomic analysis with Jupyter Notebooks.

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genepattern-server

The GenePattern Server web application

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genepattern-python

GenePattern Python Library

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AmpliconSuiteAggregator

Aggregates the results from AmpliconSuite

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RandomForest

Random Forest, GenePattern - Mesirov Lab, UCSD

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AmpliconSuite

Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.

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ComBat

Performs batch correction on a dataset containing multiple batches

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RandomForest.GPU

Random Forest GPU, GenePattern - Mesirov Lab, UCSD

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Tangram

A method for mapping sc/snRNA-seq data to various forms of spatial data collected from the same region.

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common_module_code

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

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Harmony

Wrapper Script for Harmony designed to work with GenePattern Module Integrator

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ComBat_Seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data. Credits: https://github.com/zhangyuqing/ComBat-seq

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FcsToCsv

Converts a Flow Cytometry Standard (FCS) file to a Comma Separated Values (CSV) file.

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nmf

Module for performing non-negative matrix factorization

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scVelo

scVelo wrapper module for GenePattern

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Seurat.InteractiveUMAPVisualizer

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

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tfsites.AffinityScan

Step 6 of tfsites workflow, as a GenePattern module

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tfsites.AnalyzeEQTLs

Finds all effects of SNVs from GWAS data

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tfsites.AnalyzeGenomeMPRA

AnalyzeGWAS

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tfsites.AnnotateAndVisualizeTFSites

Farley lab collaboration

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tfsites.common_docker

Docker container for all the Farley lab tfsites suite of modules

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tfsites.CompareEnhancers

Compares the two seqs and reports the binding site effect on diff seqs

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tfsites.DefineTfBindingSitesFromPBM

Farley lab UCSD collaboration

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tfsites.defineTFBindingSitesFromPFM

tfsites modules for defineBindingStites starting with Position Frequency Matrix from JASPAR

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tfsites.DifferentialBindingAnalysis

tfsites.DifferentialBindingAnalysis.py compares the e-scores between two PBM datasets.

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tfsites.InSilicoSnvAnalysis

Farley Lab UCSD Collaboration

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tfsites.IntegrateGenomeAnnotations

tfsites.IntegrateGenomeAnnotations finds all possible SNVs and their effects on binding sites.

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tfsites.LoadGenome

converts fasta file into dictionary and stores it as a pickled file.

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tfsites.VisualizePhenotypicGenotypes

Creates a visualization showing all SNV effects that overlap with genotypes

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tximport.DESeq2

tximport.DESeq2 wrapper module for GenePattern.

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