gene-sets

There are 43 repositories under gene-sets topic.

  • broadinstitute/ssGSEA2.0

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

    Language:R257133279

  • igordot/msigdbr

    MSigDB gene sets for multiple organisms in a tidy data format

    Language:R7093514

  • greenelab/BioBombe

    BioBombe: Sequentially compressed gene expression features enhances biological signatures

    Language:Jupyter Notebook6465425

  • JEFworks/liger

    Lightweight Iterative Gene set Enrichment in R

    Language:R57559

  • drostlab/myTAI

    Evolutionary Transcriptomics with R

    Language:R4161718

  • slowkow/snpsea

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

    Language:C++35359

  • epigen/enrichment_analysis

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

    Language:Python322252

  • krassowski/gsea-api

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

    Language:Python15452
  • BioCor

    llrs/BioCor

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

    Language:R144281

  • ComPath/ComPath

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

    Language:JavaScript136871
  • cinaR

    eonurk/cinaR

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

    Language:R12263

  • 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.

    Language:Jupyter Notebook12214

  • MaayanLab/Playbook-Workflow-Builder

    A repository for the Playbook Workflow Builder project.

    Language:TypeScript11215318

  • Albluca/rRoma

    An r interface to perform ROMA

    Language:R10416

  • 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).

    Language:R7721
  • covid19_crowd_library

    MaayanLab/covid19_crowd_library

    COVID-19 Crowd Generated Gene and Drug Set Library

    Language:Python641410

  • PavlidisLab/ermineR

    R wrapper for ermineJ

    Language:R63244

  • greenelab/annotation-refinery

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

    Language:Python5592

  • llrs/GSEAdv

    Package to analyse gene sets

    Language:R53201
  • GSECA

    matteocereda/GSECA

    Gene Set Enrichment Class Analysis for heterogeneous RNA sequencing data

    Language:R5321

  • slowkow/xlmhg

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

    Language:C++5301

  • unistbig/GScluster

    gene-set clustering and network visualization

    Language:JavaScript5343

  • EMSL-Computing/TMSig

    An R package containing tools to prepare, analyze, and visualize named lists of sets, with an emphasis on molecular signatures (such as gene sets).

    Language:R4420
  • cinaR-genesets

    eonurk/cinaR-genesets

    Ready-to-use curated genesets for cinaR

    Language:R3201

  • greenelab/tribe

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

    Language:Python36253

  • chiarabales/geneset_SV

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

    Language:Python2100

  • diyadas/HBC-regen

    Code and resources related to the olfactory regeneration project

    Language:R2303

  • 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

    Language:HTML2101

  • sartorlab/chipenrich.data

    Experimental version of data package associated with chipenrich

    Language:R2712

  • 3inar/geneset

    Gene sets and functions for working with them.

    Language:R1202

  • DBRetina/DBRetina

    DBRetina python package

    Language:C++1291

  • markziemann/cistro_gmt

    enabling pathway analysis of curated chip-seq data

    Language:Shell1300

  • MoseleyBioinformaticsLab/categoryCompare2

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

    Language:R12381

  • ELTEbioinformatics/GMT_files_for_mulea

    GMT files for the mulea R package

    Language:Python02130

  • ELTEbioinformatics/muleaData

    muleaData is an ExperimentHubData Bioconductor package for the mulea R package

    Language:R0301

  • markziemann/dee2_gene_signatures

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

    Language:R216