enrichment-analysis

There are 5 repositories under enrichment-analysis topic.

YuLab-SMU / clusterProfiler
:bar_chart: A universal enrichment tool for interpreting omics data
enrichment-analysis go gsea kegg rstats visualization
Language:R 944
gget
pachterlab / gget
🧬 gget enables efficient querying of genomic reference databases
alphafold2 databases enrichment-analysis ensembl gget ncbi reference uniprot alphafold archs4 blast enrichr
Language:Python 864
zqfang / GSEApy
Gene Set Enrichment Analysis in Python
enrichment-analysis gsea python3 rust
Language:Python 506
YuLab-SMU / enrichplot
Visualization of Functional Enrichment Result
visualization enrichment-analysis pathway-analysis
Language:R 216
saezlab / decoupler-py
Python package to perform enrichment analysis from omics data.
bioinformatics data-science enrichment enrichment-analysis numba python single-cell spatial-transcriptomics transcriptomics
Language:Python 138
YuLab-SMU / DOSE
:mask: Disease Ontology Semantic and Enrichment analysis
disease-ontology enrichment-analysis semantic-similarity
Language:R 105
igordot / msigdbr
MSigDB gene sets for multiple organisms in a tidy data format
genomics msigdb gene-sets pathways gsea pathway-analysis enrichment-analysis
Language:R 64
YuLab-SMU / biomedical-knowledge-mining-book
:books: Biomedical knowledge mining using GOSemSim and clusterProfiler
gene-ontology semantic-similarity enrichment-analysis disease-ontology medical-subject-headings clusterprofiler gosemsim
Language:TeX 64
GangLiLab / genekitr
🧬 Gene analysis toolkit based on R
gene enrichment-analysis id-converter plotting
Language:R 50
stephenslab / rss
Regression with Summary Statistics.
bayesian-methods enrichment-analysis gene-prioritization genetic-associations gwas-summary-statistics heritability mcmc variational-inference
Language:MATLAB 46
sk-sahu / sig-bio-shiny
A standalone interactive application for detecting biological significance on a set of genes
sig-bio-shiny enrichment-analysis annotationhub gene-list non-model-species gene-ontology kegg-pathway data-visualization shiny shiny-apps gene
Language:R 40
baryshnikova-lab / safepy
Python implementation of Spatial Analysis of Functional Enrichment (SAFE)
network-analysis enrichment-analysis bioinformatics computational-biology
Language:Python 37
YuLab-SMU / ReactomePA
Reactome Pathway Analysis
enrichment-analysis reactome-pathway-analysis reactomepa
Language:R 36
stracquadaniolab / pygna
A Python package for gene network analysis
network-biology networkx enrichment-analysis pygna biostatistics bioinformatics
Language:Python 32
amarinderthind / RNA-seq-tutorial-for-gene-differential-expression-analysis
This tutorial is created for educational purpose
rnaseq-pipeline rnaseq rnaseq-workshop deseq2 edger enrichment-analysis bioconductor-packages reactome-pathway pca-analysis rna-seq-dge tutorial gene-expression analysis rna-seq r ngs ngs-analysis
Language:R 27
kerseviciute / aPEAR
Enrichment Networks for Pathway Enrichment Analysis
clustering enrichment enrichment-analysis gsea network pathway plot r visualization
Language:R 27
Danko-Lab / rtfbs_db
Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
transcription-factors transcription-factor-binding motif tfbs-discovery enrichment-analysis cis-bp r
Language:R 22
GeneSCF
genescf / GeneSCF
Gene Set Clustering based on Functional annotation
cancer download-ontology download-pathways enrichment-analysis enrichment-testing functional-enrichment functional-enrichment-analysis gene gene-set-analysis gene-set-clustering gene-set-enrichment geneontology gsea kegg-pathway reactome-pathway real-time up-to-date
Language:Perl 21
Kumquatum / GWENA
Gene Co-expression Network analysis pipeline
co-expression gene network-analysis enrichment-analysis transcriptomics pipeline
Language:R 21
decodebiology / geneSCF_inactive
GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF
gene-set-clustering enrichment-analysis gene-annotation gene-ontology kegg kegg-pathway kegg-gene pathways pathway-analysis reactome functional-analysis real-time-processing real-time-analytics
Language:Perl 20
allielarocco / Microarray-Analysis
Microarray Analysis Pipeline in Python
differential-expression differentially-expressed-genes enrichment-analysis microarray microarray-experiments microarray-studies ncbi-database ncbi-geo ncbi-submission pipeline
Language:Jupyter Notebook 18
gladstone-institutes / Interactive-Enrichment-Analysis
A set of Shiny apps to provide interactive enrichment analysis and exploration of results.
bioinformatics enrichment-analysis foss openscience shiny
Language:R 18
moosa-r / rbioapi
rbioapi: User-Friendly R Interface to Biologic Web Services' API
api-client bioinformatics biology cran enrichment-analysis r rstats rstats-package jaspar over-representation-analysis panther reactome mieaa enrichr string uniprot enrichment
Language:R 17
saramasarone / enrich_omics
A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)
omics enrichment enrichment-analysis genomics proteomics drug-discovery drug-repurposing transcriptomics omics-data targets enrichr opentargets
Language:Python 17
SUwonglab / rss-net
Regression with Summary Statistics exploiting Network Topology.
gwas-summary-statistics gene-regulatory-network bayesian-methods variational-inference gene-prioritization enrichment-analysis
Language:R 17
epigen / enrichment_analysis
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
bioinformatics genomic-regions enrichment-analysis atac-seq biomedical-data-science chip-seq gene-set-enrichment gene-sets rna-seq visualization pipeline snakemake workflow
Language:Python 14
Kuanhao-Chao / RNASeqR
📊 An R package of RNA-seq workflow
alignment bioconductor differential-gene-expression enrichment-analysis pipeline quality-control r rnq-seq workflow
Language:R 14
BgeeDB / BgeeDB_R
Source code of the R packge BgeeDB to use data from the Bgee database
bioinformatics enrichment-analysis rna-seq scrna-seq single-cell
Language:R 13
unistbig / netGO
R/Shiny package for network-integrated pathway enrichment analysis
r network-analysis netgo shinyapps protein-protein-interaction enrichment-analysis
Language:R 13
AllEnricher
zd105 / AllEnricher
A comprehensive gene set function enrichment tool for multiple species.
kegg do disease enrichment-analysis non-model-species go
Language:Shell 13
harryhaller001 / keggtools
Library for KEGG pathway enrichment analysis
enrichment-analysis kegg kegg-pathway python
Language:Python 12
remap-cisreg / ReMapEnrich
ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnrich provide functions to import any in-house catalogue, automate and plot the enrichment analysis for genomic regions.
r genomic-regions chip-seq enrichment-analysis transcription-factor-binding r-package
Language:HTML 12
soumitag / SLIDE
A visualization tool for Systems-Level Interactive Data Exploration
visualization omics large-scale-data-visualization heatmap hierarchical-clustering interactive-visualizations web-based-visualization gene-expresssion enrichment-analysis
Language:Java 12
cinaR
eonurk / cinaR
A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)
atac-seq unknown-batch-effects edger deseq2 limma differential-analysis enrichment-analysis genesets gene-sets r r-package
Language:R 11
ELTEbioinformatics / mulea
mulea - an R package for enrichment analysis using various ontologies and empirical FDR correction
bioconductor-package enrichment enrichment-analysis functional-enrichment-analysis gene-set-enrichment ontologies r-package transcriptomics
Language:R 10
YuLab-SMU / meshes
:stethoscope: MeSH Enrichment and Semantic analyses
medical-subject-headings semantic-similarity enrichment-analysis
Language:R 9