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IngoScholtes / pathpy

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pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models

python data machine-learning data-mining graph analysis model-selection networks temporal-networks graphical-models pathways network-analysis sequential-data multi-order temporal-correlations

Updated May 2, 2020
Python

Caleydo / caleydo

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Caleydo - Visualization for Molecular Biology

visualization eclipse pathways gehlenborglab caleydo

Updated Dec 15, 2016
Java

iVis-at-Bilkent / newt

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A web application to visualize and edit pathway models

visualization editor bioinformatics biology layout systems-biology pathways network-visualization pathway-analysis newt web-based-visualization sbml sbgn sif pathway-models celldesigner

Updated Aug 14, 2021
JavaScript

igordot / msigdbr

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MSigDB gene sets for multiple organisms in a tidy data format

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

Updated May 5, 2021
R

iVis-at-Bilkent / pathway-mapper

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PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

bioinformatics systems-biology tcga cancer-genomics pathways network-visualization pathway-analysis cancer-pathways

Updated Jul 11, 2021
TypeScript

saezlab / OmnipathR

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R client for the OmniPath web service

proteins networks pathways complexes networks-biology omnipath enzyme-ptm

Updated Aug 9, 2021
R

iVis-at-Bilkent / sbgnviz.js

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A web based visualization tool for process description maps in SBGN

bioinformatics systems-biology pathways network-visualization sbgn

Updated Jul 16, 2021
JavaScript

geneontology / noctua

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Graph-based modeling environment for biology, including prototype editor and services

annotation owl ontology pathways curation geneontology functional-annotation noctua noctua-models go-cam

Updated Aug 11, 2021
JavaScript

JuliaOcean / AIBECS.jl

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The ideal tool for exploring global marine biogeochemical cycles.

Updated Aug 13, 2021
Julia

Caleydo / pathfinder

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Pathfinder is a tool for the visual exploration of paths in large graphs.

pathfinder pathways phovea phovea-application

Updated Aug 28, 2018
JavaScript

decodebiology / geneSCF_inactive

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GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF

gene-annotation gene-ontology pathways kegg pathway-analysis reactome kegg-pathway real-time-analytics enrichment-analysis real-time-processing functional-analysis kegg-gene gene-set-clustering

Updated Oct 30, 2020
Perl

PathwayAndDataAnalysis / causalpath

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A project for exploring differentially active signaling paths related to proteomics datasets

bioinformatics computational-biology proteomics pathways phosphoproteomics causality-analysis pathway-analysis

Updated Jul 18, 2021
Java

jdrudolph / photon

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PHOsphoproteomic dissecTiOn using Networks

linux bioinformatics biology proteomics biological-data-analysis signaling-pathways pathways phosphoproteomics phosphorylation signaling-networks

Updated Jan 25, 2021
Python

iVis-at-Bilkent / chise.js

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A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

editor bioinformatics biology systems-biology pathways network-visualization pathway-analysis sbgn

Updated Jul 12, 2021
JavaScript

llrs / BioCor

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

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

Updated Apr 26, 2021
R

PathwayMerger / PathMe

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Harmonizing pathway databases using Biological Expression Language (BEL)

bioinformatics systems-biology pathways pathway-analysis biological-expression-language

Updated Apr 13, 2021
Python

utkarshxy / 100-days-of-Data-Science

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This is the complete module you will need to get started with 100 days of Data Science by 100 days Official.

data-science journey pathways

Updated May 13, 2021
HTML

greenelab / tad_pathways_pipeline

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Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

workflow gwas analysis candidate-genes tad methodology pathways tads

Updated Dec 21, 2019
Python

bio2bel / kegg

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A Bio2BEL package for integrating pathway-related information from KEGG in BEL

proteins systems-biology pathways kegg biological-expression-language networks-biology

Updated Nov 21, 2020
Python

wikipathways / rWikiPathways

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R package for WikiPathways API

bioinformatics pathways data-access rpackage

Updated May 19, 2021
R

geneontology / noctua-models

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This is the data repository for the models created and edited with the Noctua tool stack for GO.

annotation ontology pathways geneontology noctua-models go-cam

Updated Aug 14, 2021
Makefile

ComPath / compath-resources

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This repository contains the different resources derived or generated using ComPath

bioinformatics pathways jupyter-notebooks mappings pathway-analysis curation system-biology

Updated Jul 27, 2021
Jupyter Notebook

ComPath / ComPath

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Open

Add tutorial with screenshot and videos

ddomingof opened Mar 6, 2018

good first issue

PathwayAnalysisPlatform / PathwayMatcher_Dev

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PathwayMatcher is a free, open-source software to search for pathways related to a list of proteins in Reactome. This repository is the development repository. For the latest version see: https://github.com/PathwayAnalysisPlatform/PathwayMatcher

development pathways pathway-analysis reactome biological-networks proteoforms

Updated Mar 4, 2019
Java

rosscm / fedup

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🎣 Bioconductor package for pathway enrichment and depletion analysis via a Fisher's exact test on custom test sets and annotations

enrichment network bioconductor pathways

Updated Jul 12, 2021
R

ps4dr / ps4dr

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Pathway Signatures for Drug Repositioning and Discovery

workflow bioinformatics drug-discovery drug-repurposing pathways multi-modal-data

Updated Jul 15, 2020
HTML

bio2bel / reactome

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Integration of pathway-related information from Reactome in BEL

pathways reactome biological-expression-language networks-biology system-biology

Updated Nov 18, 2020
Python

PathwayMerger / PathMe-Viewer

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A web application for visualizing and exploring pathway knowledge in Biological Expression Language (BEL)

visualization bioinformatics pathways network-visualization pathway-analysis networks-biology

Updated Jan 9, 2020
JavaScript

geneontology / pathways2GO

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Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)

ontology pathways geneontology biopax go-cam

Updated Jun 17, 2021
Java

geneontology / gocam-sif-pyexport

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Export GO-CAMs to SIF (Python)

annotations cytoscape pathways geneontology go-cam

Updated Mar 28, 2021
Python

pathways

Here are 73 public repositories matching this topic...

IngoScholtes / pathpy

Caleydo / caleydo

iVis-at-Bilkent / newt

igordot / msigdbr

iVis-at-Bilkent / pathway-mapper

saezlab / OmnipathR

iVis-at-Bilkent / sbgnviz.js

geneontology / noctua

JuliaOcean / AIBECS.jl

Caleydo / pathfinder

decodebiology / geneSCF_inactive

PathwayAndDataAnalysis / causalpath

jdrudolph / photon

iVis-at-Bilkent / chise.js

llrs / BioCor

PathwayMerger / PathMe

utkarshxy / 100-days-of-Data-Science

greenelab / tad_pathways_pipeline

bio2bel / kegg

wikipathways / rWikiPathways

geneontology / noctua-models

ComPath / compath-resources

ComPath / ComPath

Add tutorial with screenshot and videos

PathwayAnalysisPlatform / PathwayMatcher_Dev

rosscm / fedup

ps4dr / ps4dr

bio2bel / reactome

PathwayMerger / PathMe-Viewer

geneontology / pathways2GO

geneontology / gocam-sif-pyexport

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