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Projects in Awesome Lists tagged with pathway-analysis

A curated list of projects in awesome lists tagged with pathway-analysis .

https://github.com/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.

alternative-splicing bam-files bioinformatics-pipeline cell-cycle cell-type-classification clustering command-line-tool fastq-anaysis graphical-interface louvain-community-detection marker-gene-analysis network-analysis pagerank pathway-analysis python rna-seq-data scrna-seq-data single-cell-splicing splicing-quantification splicing-visualization

Last synced: 09 Apr 2026

https://github.com/igordot/msigdbr

MSigDB gene sets for multiple organisms in a tidy data format

enrichment-analysis gene-sets genomics gsea msigdb pathway-analysis pathways

Last synced: 19 Feb 2026

https://github.com/iiasa/ipcc_sr15_scenario_analysis

Scenario analysis notebooks for the IPCC Special Report on Global Warming of 1.5°C

climate-change climate-change-mitigation integrated-assessment ipcc pathway-analysis scenario sr15

Last synced: 18 Jan 2026

https://github.com/cxli233/ggpathway

A tutorial for pathway visualization using tidyverse, igraph, and ggraph

data-visualization pathway-analysis r

Last synced: 12 Apr 2025

https://github.com/reactome/reactome2py

python client for reactome content, analysis, and human functional protein interactions (FI) services api calls.

enrichment pathway-analysis pypi python-client reactome-data-content visualization

Last synced: 11 Mar 2026

https://github.com/futianfan/genocraft

GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)

bulk-rna-seq flask genomics multiomics next-generation-sequencing ngs omics omics-data-integration pathway-analysis protein rna-seq single-cell visualization

Last synced: 12 Oct 2025

https://github.com/markziemann/mitch

An R package for multi-dimensional pathway enrichment analysis

gene-regulation gene-seq-analysis pathway-analysis

Last synced: 18 Feb 2026

https://github.com/llrs/biocor

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

bioconductor-packages bioinformatics functional-similarity gene gene-sets pathway-analysis pathways similarity similarity-measurement

Last synced: 21 Sep 2025

https://github.com/krassowski/gsea-api

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

bioinformatics cuda enrichment gene-set-enrichment gene-sets gsea pandas pathway-analysis python3 transcriptomics

Last synced: 13 Apr 2025

https://github.com/pathwayforte/pathway-forte

A Python package for benchmarking pathway database with functional enrichment and classification methods

benchmarking bioinformatics databases machine-learning pathway-analysis pathway-enrichment-analysis systems-biology

Last synced: 17 Jun 2025

https://github.com/sales-lab/graphite

GRAPH Interaction from pathway Topological Environment

bioinformatics mirror pathway-analysis pathways r

Last synced: 09 Jan 2026

https://github.com/greenelab/pathcore-t-analysis

This repository is in support of the PathCORE-T paper (https://doi.org/10.1101/147645). It contains all the code and necessary data/metadata to repeat all analyses in the paper.

feature-extraction gene-expression pathway-analysis supplement

Last synced: 05 May 2025

https://github.com/greenelab/gea_community_detection

Overrepresentation analysis for KEGG and PID pathways using community detection

analysis detection-network enrichment-analysis gene-expression kegg-pathway networks pathway pathway-analysis pid

Last synced: 05 May 2025

https://github.com/pathwayforte/results

Results of the evaluation of pathway databases using TCGA datasets

benchmarking bioinformatics database pathway-analysis systems-biology

Last synced: 12 Apr 2025

https://github.com/bio2bel/msig

Integration of pathway-related information from MSigDB in BEL

gene-set-enrichment msig msigdb pathway-analysis

Last synced: 29 Jan 2026

https://github.com/prody/comd

This package runs collective molecular dynamics simulations, where collective motions from anisotropic network model normal mode analysis drive all-atom dynamics through targeted molecular dynamics simulations and energy minimization

anm comd pathway-analysis sampling-methods simulations

Last synced: 06 Apr 2026

https://github.com/baderlab/poppathr

Population-based pathway analysis of SNP-SNP coevolution

coevoluton enrichment pathway-analysis population-genetics positive-selection

Last synced: 08 Apr 2025

https://github.com/mizcausevic-dev/curriculum-knowledge-graph

Curriculum graph for courses, prerequisites, skills, outcomes, and pathway bottleneck analysis in higher education.

curriculum edtech education-data fastapi graph-modeling higher-education knowledge-graph learning-design pathway-analysis python skills

Last synced: 01 Jun 2026

https://github.com/llrs/pathways-study

Analyze and compare different pathway resources

bioinformatics pathway-analysis

Last synced: 08 Apr 2025

https://github.com/bibymaths/bachelor_thesis

Identification of Potent Biomarkers for Prostate Cancer Through AR, Mapk and M-TOR Signaling Pathways Mining

bachelor bioinformatics cancer pathway-analysis prostate-cancer thesis

Last synced: 23 Mar 2025

https://github.com/drmsabdullahi/genpath-pph

GenPath-PPH: Python package for integrating gene expression and KEGG pathway networks via Persistent Path Homology to detect disease-relevant pathway dysregulation. Available on PyPI: pip install genpath-pph

bioinformatics pathway-analysis pathway-enrichment-analysis persistent-homology persistent-path-homology topological-data-analysis

Last synced: 24 May 2026