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: 08 Apr 2025

https://github.com/federicomarini/genetonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

bioconductor bioconductor-package data-exploration data-visualization functional-enrichment-analysis gene-expression gui pathway-analysis r reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome transcriptomics user-friendly

Last synced: 13 Apr 2025

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: 27 Nov 2024

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/dvklopfenstein/reactomepy

Explore biomolecular pathways in Reactome from the command-line or a Python script

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool biological-networks biotech biotechnology molecular-biology pathway-analysis pathway-enrichment-analysis pathway-models protein-protein-interaction reactome reactome-pathway

Last synced: 21 Mar 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/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: 13 Jan 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: 19 Dec 2024

https://github.com/iVis-at-Bilkent/syblars

SyBLaRS: Systems Biology Layout & Rendering Service

bioinformatics graph-algorithms graph-drawing graphviz network-visualization pathway-analysis pathways systems-biology

Last synced: 09 May 2025

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

GRAPH Interaction from pathway Topological Environment

bioinformatics mirror pathway-analysis pathways r

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/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