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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: 08 Nov 2024

https://github.com/genepattern/gistic_2.0

Genomic Identification of Significant Targets in Cancer

genepattern-module snp-analysis

Last synced: 08 Nov 2024

https://github.com/genepattern/hierarchicalclustering

GenePattern Hierarchical Clustering module.

genepattern-module

Last synced: 08 Nov 2024

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: 08 Nov 2024

https://github.com/genepattern/stream.preprocess

Step one of the STREAM ssRNA-Seq Trajectory pipeline

genepattern-module rna-seq single-cell

Last synced: 08 Nov 2024

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: 08 Nov 2024

https://github.com/genepattern/stream.visualizetrajectories

Generate the signature subway and stream plots

genepattern-module rna-seq single-cell

Last synced: 08 Nov 2024

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: 08 Nov 2024

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: 08 Nov 2024

https://github.com/genepattern/hisat2.aligner

Repo for the dockerized HISAT2.aligner module

bioinformatics genepattern-module rna-seq

Last synced: 08 Nov 2024

https://github.com/genepattern/tcga.sampleselection

TCGA.SampleSelection wrapper module for GenePattern.

genepattern-module msigdb preprocess tcga utilities

Last synced: 08 Nov 2024

https://github.com/genepattern/opencravat

OpenCRAVAT as a GenePattern module

genepattern-module variant-annotation

Last synced: 08 Nov 2024

https://github.com/genepattern/hierarchicalclusteringviewer

Views results of hierarchical clustering.

genepattern-module visualizer

Last synced: 08 Nov 2024

https://github.com/genepattern/htseq.count

HTSeq (0.11.2) wrapper module: Counting reads in features with 'htseq-count'

genepattern-module rna-seq

Last synced: 08 Nov 2024

https://github.com/genepattern/deseq2toodf

This module will turn a TXT file into ComparativeMarkerSelectionViewer-compatible ODF file

conversion genepattern-module utilities

Last synced: 08 Nov 2024

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: 08 Nov 2024

https://github.com/genepattern/heatmapviewer

A configurable heat map viewer that provides users with several options for manipulating and visualizing array-based data

genepattern-module visualizer

Last synced: 08 Nov 2024

https://github.com/genepattern/mutpanning

Docker . module for the single cell toolkit

genepattern-module mutational-significance-analysis

Last synced: 08 Nov 2024

https://github.com/genepattern/clsfilecreator

This a GenePattern Javascript visualizer that creates a CLS file from a GCT file.

genepattern-module visualizer

Last synced: 08 Nov 2024

https://github.com/genepattern/geoimporter

Imports data from the Gene Expression Omnibus (GEO)

genepattern-module preprocess utility

Last synced: 08 Nov 2024

https://github.com/genepattern/esppredictor

Determine which tryptic peptides will generate the highest signal in ESI-MS

genepattern-module proteomics

Last synced: 08 Nov 2024

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: 08 Nov 2024

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: 08 Nov 2024

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: 08 Nov 2024

https://github.com/genepattern/predictionresultsviewer

Visualizes prediction results

genepattern-module visualizer

Last synced: 08 Nov 2024

https://github.com/genepattern/igv.js

GenePattern module wrapping igv.js

genepattern-module igv

Last synced: 08 Nov 2024

https://github.com/genepattern/salmon.indexer

Salmon indexer wrapper module for GenePattern.

genepattern-module preprocess-and-utilities rna-seq

Last synced: 08 Nov 2024

https://github.com/genepattern/discover

GenePattern Module which implements the DiSCoVER algorithm

drug-repurposing genepattern-module prediction rna-seq

Last synced: 08 Nov 2024

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: 08 Nov 2024

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: 08 Nov 2024

https://github.com/genepattern/differentialexpressionviewer

Visualizes the results of ComparativeMarkerSelection

differential-expression genepattern-module javascript visualizer

Last synced: 08 Nov 2024

https://github.com/genepattern/stream.detectleafgenes

Detect marker genes that distinguish the different trajectories

genepattern-module rna-seq single-cell

Last synced: 08 Nov 2024

https://github.com/genepattern/stream.detectdifferentiallyexpressedgenes

Detect differentially expressed genes between pairs of trajectory branches

genepattern-module rna-seq single-cell

Last synced: 08 Nov 2024

https://github.com/genepattern/stream.detecttransitiongenes

Detect transition genes for each branch of the trajectory.

genepattern-module rna-seq single-cell

Last synced: 08 Nov 2024