gene-sets

There are 1 repository under gene-sets topic.

• broadinstitute / ssGSEA2.0

  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

  ptm-seaptm-signaturesptm-sitespathway-enrichment-analysisgene-setsgseakseaptm-enrichment-analysisphosphoproteomics
  Language:R 223

• igordot / msigdbr

  MSigDB gene sets for multiple organisms in a tidy data format

  genomicsmsigdbgene-setspathwaysgseapathway-analysisenrichment-analysis
  Language:R 64

• greenelab / BioBombe

  BioBombe: Sequentially compressed gene expression features enhances biological signatures

  gene-setsmsigdbgene-expressiontcgacompressionhetnetbiobombenetworkautoencoder
  Language:Jupyter Notebook 63

• JEFworks / liger

  Lightweight Iterative Gene set Enrichment in R

  bioinformaticsgseaenrichmentrstatsgene-setspathway-enrichment-analysiscran
  Language:R 55

• drostlab / myTAI

  Evolutionary Transcriptomics with R

  evolutionary-transcriptomicsrtranscriptomeevolutionevo-devostudies-transcriptomesbiological-processesgene-setsmytaigene-expressionconservationexpression-profiles
  Language:R 36

• slowkow / snpsea

  :bar_chart: Identify cell types and pathways affected by genetic risk loci.

  risk-locigenetissuegene-setsalgorithmenrichmentgwasbioinformatics
  Language:C++ 34

• epigen / enrichment_analysis

  A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.

  bioinformaticsgenomic-regionsenrichment-analysisatac-seqbiomedical-data-sciencechip-seqgene-set-enrichmentgene-setsrna-seqvisualizationpipelinesnakemakeworkflow
  Language:Python 18

• krassowski / gsea-api

  Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)

  gseacudapandaspython3gene-set-enrichmentbioinformaticstranscriptomicspathway-analysisgene-setsenrichment
  Language:Python 14
• BioCor

  llrs / BioCor

  Package to calculate functional similarity between genes https://biocor.llrs.dev

  similarity-measurementsimilarityfunctional-similaritybioinformaticspathway-analysisgene-setsbioconductor-packagesgenepathways
  Language:R 14

• ComPath / ComPath

  A web application for exploring, analyzing, and curating pathway databases

  pathwaysgene-setssystems-biologypathway-analysisbioinformaticsbioinformatics-databases
  Language:JavaScript 11
• cinaR

  eonurk / cinaR

  A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)

  atac-sequnknown-batch-effectsedgerdeseq2limmadifferential-analysisenrichment-analysisgenesetsgene-setsrr-package
  Language:R 11

• Albluca / rRoma

  An r interface to perform ROMA

  romarexpression-matrixgene-setsgmt
  Language:R 10

• lab-conrad / resVAE

  resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.

  single-cellsingle-cell-analysissingle-cell-omicssingle-cell-sequencingsingle-cell-rna-seqgene-setsgene-expressionnature-machine-intelligence
  Language:Jupyter Notebook 10

• kmezhoud / canceR

  :chart: The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

  cancercancer-datagenegene-expressiongene-methylationgene-mutationgene-setsmethylationmskccmutationsrtcltk
  Language:R 7
• covid19_crowd_library

  MaayanLab / covid19_crowd_library

  COVID-19 Crowd Generated Gene and Drug Set Library

  drug-setsgene-setscovid-19covid19-data
  Language:Python 6

• PavlidisLab / ermineR

  R wrapper for ermineJ

  ogan-biogene-setsbioinformaticsgenomicsbiologyenrichment-analysis
  Language:R 6

• xiangzhu / rss-gsea

  Full results to accompany Zhu and Stephens (2018).

  variational-inferencegwas-summary-statisticsbayesian-methodsgene-prioritizationenrichment-analysisbiological-pathwaysgene-sets
  Language:R 6

• greenelab / annotation-refinery

  A python package that consists of functions that process publicly available annotated sets of genes

  toolscriptpackagegene-setsontology
  Language:Python 5

• llrs / GSEAdv

  Package to analyse gene sets

  bioconductorgene-setspathway-analysis
  Language:R 5
• GSECA

  matteocereda / GSECA

  Gene Set Enrichment Class Analysis for heterogeneous RNA sequencing data

  rna-sequencinghandiling-heteogeneitygene-set-analysisbig-databig-data-analyticsgseavariance-analysisfinite-mixturegene-setsdata-discretizationfmmcohortstcgapancancer
  Language:R 5

• slowkow / xlmhg

  :chart_with_downwards_trend: Non-parametric rank enrichment test for binary data.

  rrcppenrichmentbioinformaticsgene-sets
  Language:C++ 5

• unistbig / GScluster

  gene-set clustering and network visualization

  cytoscapejsgene-setsnetwork-visualizationshiny-rweighted-graphs
  Language:JavaScript 5
• cinaR-genesets

  eonurk / cinaR-genesets

  Ready-to-use curated genesets for cinaR

  genesetswikipathwaysdiceenrichmentenrichment-analysispbmcgene-sets
  Language:R 3

• greenelab / tribe

  An open-source webserver that allows for easy, reproducible genomics analyses between different webservers

  serverweb-servertoolgene-sets
  Language:Python 3

• chiarabales / geneset_SV

  Reference implementation of the paper Redundancy-aware unsupervised ranking based on game theory - application to gene enrichment analysis

  game-theorygene-setsoverlapping-genespathwaysredundancy-reductionshapley-valuesunsupervised-feature-selection
  Language:Python 2

• diyadas / HBC-regen

  Code and resources related to the olfactory regeneration project

  single-cell-rna-seqnormalizationcluster-analysistranscription-factorsgene-setsvisualizationlineage-trajectoryslingshotgene-expressiondifferential-expressionclustering
  Language:R 2

• 3inar / geneset

  Gene sets and functions for working with them.

  genomicstranscriptomicsgene-setsbloodsignature
  Language:R 1

• DBRetina / DBRetina

  DBRetina python package

  enrichment-analysisgenegene-set-enrichmentgene-setsgenesorapathwaysdeduplicationgseaover-representation-analysisset-cover
  Language:C++ 1

• EMSL-Computing / TMSig

  Tools to prepare and analyze a priori molecular signatures, such as gene sets.

  rr-packagegene-setsmolecular-signatures
  Language:R 1

• markziemann / cistro_gmt

  enabling pathway analysis of curated chip-seq data

  gene-regulationchip-seqgene-setsgene-set-analysis
  Language:Shell 1

• MoseleyBioinformaticsLab / categoryCompare2

  Enables Gene Ontology (and other feature annotation) enrichment calculations and comparisons between feature sets.

  bioconductorbioinformaticsrgene-expressiongene-setsgene-annotationrstats
  Language:R 1

• sartorlab / chipenrich.data

  Experimental version of data package associated with chipenrich

  chip-seqgene-set-enrichmentgene-sets
  Language:R 1

• ELTEbioinformatics / GMT_files_for_mulea

  GMT files for the mulea R package

  gene-set-enrichmentgene-setsontologies
  Language:Python 0

• ELTEbioinformatics / muleaData

  muleaData is an ExperimentHubData Bioconductor package for the mulea R package

  bioconductor-packageenrichment-analysisgene-setsontologies
  Language:R 0

• MolecularPathologyLab / SubtypeExploreR

  Web application that enables users to compare the expression of genes or enrichment of gene sets between different molecular subtypes of colorectal cancer

  enrichment-analysisgene-expressiongene-expression-signaturesgene-set-enrichment-analysisgene-setsgseapathway-enrichment-analysisrshiny
  Language:HTML 0

• markziemann / dee2_gene_signatures

  A resource of gene expression signatures derived from the DEE2 dataset (http://dee2.io)

  gene-setsgene-set-analysisdata-mininggene-regulationgenomics
  Language:R