pathway-analysis
There are 95 repositories under pathway-analysis topic.
YuLab-SMU/enrichplot
Visualization of Functional Enrichment Result
nsalomonis/altanalyze
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
federicomarini/GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
igordot/msigdbr
MSigDB gene sets for multiple organisms in a tidy data format
iiasa/ipcc_sr15_scenario_analysis
Scenario analysis notebooks for the IPCC Special Report on Global Warming of 1.5°C
jackbibby1/SCPA
R package for pathway analysis in scRNA-seq data
iVis-at-Bilkent/pathway-mapper
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
iVis-at-Bilkent/newt
A web application to visualize and edit pathway models
cxli233/ggpathway
A tutorial for pathway visualization using tidyverse, igraph, and ggraph
PathwayAndDataAnalysis/causalpath
A project for exploring differentially active signaling paths related to proteomics datasets
qbic-pipelines/rnadeseq
Differential gene expression analysis and pathway analysis of RNAseq data
raeslab/omixer-rpm
A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.
reactome/reactome2py
python client for reactome content, analysis, and human functional protein interactions (FI) services api calls.
mims-harvard/pathways
Disease pathways in the human interactome
dvklopfenstein/ReactomePy
Explore biomolecular pathways in Reactome from the command-line or a Python script
decodebiology/geneSCF_inactive
GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF
PathwayMerger/PathMe
Harmonizing pathway databases using Biological Expression Language (BEL)
raeslab/GMMs
A manually curated database of human gut metabolic modules.
markziemann/mitch
An R package for multi-dimensional pathway enrichment analysis
iVis-at-Bilkent/chise.js
A web application to visualize and edit the pathway models represented by SBGN Process Description Notation
krassowski/gsea-api
Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)
futianfan/GenoCraft
GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)
llrs/BioCor
Package to calculate functional similarity between genes https://biocor.llrs.dev
ComPath/ComPath
A web application for exploring, analyzing, and curating pathway databases
LucasESBS/vega
VEGA: VAE Enhanced by Gene Annotations
pathwayforte/pathway-forte
A Python package for benchmarking pathway database with functional enrichment and classification methods
iVis-at-Bilkent/syblars
SyBLaRS: Systems Biology Layout & Rendering Service
cwieder/py-ssPA
Single sample pathway analysis tools for omics data
lemaslab/rump
A Reproducible Untargeted Metabolomics Data Processing Pipeline
AlexsLemonade/refinebio-examples
Example workflows for refine.bio data
NKI-CCB/flexgsea-r
Flexible gene set enrichment analysis
omixer/omixer-rpmR
An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles
CCBR/MAAPster
MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data
collaborativebioinformatics/Disease_subsetting
Colorectal cancer CMs subtyping and personalized medication recommendation based on RNA seq pathway analysis
malhamdoosh/EGSEA
This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.
Micromeda/pygenprop
A python library for programmatic usage of EBI InterPro Genome Properties.