pathways

There are 3 repositories under pathways topic.

• IngoScholtes / pathpy

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

  temporal-networkspathwaysanalysissequential-datadatadata-miningpythonnetwork-analysisnetworksgraphmodel-selectionmachine-learninggraphical-modelsmulti-ordertemporal-correlations
  Language:Python 138

• saezlab / OmnipathR

  R client for the OmniPath web service

  omnipathcomplexesproteinsenzyme-ptmpathwaysnetworksnetworks-biology
  Language:R 88

• igordot / msigdbr

  MSigDB gene sets for multiple organisms in a tidy data format

  genomicsmsigdbgene-setspathwaysgseapathway-analysisenrichment-analysis
  Language:R 64

• Caleydo / caleydo

  Caleydo - Visualization for Molecular Biology

  visualizationgehlenborglabpathwayscaleydoeclipse
  Language:Java 58

• iVis-at-Bilkent / pathway-mapper

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

  systems-biologypathwayspathway-analysiscancer-pathwayscancer-genomicsnetwork-visualizationtcgabioinformaticsgraphviz
  Language:TypeScript 55

• iVis-at-Bilkent / newt

  A web application to visualize and edit pathway models

  pathwayspathway-analysisnetwork-visualizationeditorbioinformaticssystems-biologybiologysbgnweb-based-visualizationvisualizationpathway-modelsnewtcelldesignersiflayoutsbml
  Language:JavaScript 50

• JuliaOcean / AIBECS.jl

  The ideal tool for exploring global marine biogeochemical cycles.

  oceanoceanographyocean-circulationmodelingmodelmodelsglobaloptimizationinverse-modelmarinemarine-tracertracertransportjuliaawesomebiogeochemistrybiogeochemicalbiogeochemical-modelpathwaysfluxes
  Language:Julia 36

• geneontology / noctua

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

  noctuaowlgo-camgeneontologypathwayscurationontologynoctua-modelsfunctional-annotationannotation
  Language:JavaScript 35

• iVis-at-Bilkent / sbgnviz.js

  A web based visualization tool for process description maps in SBGN

  systems-biologypathwayssbgnbioinformaticsnetwork-visualization
  Language:JavaScript 35

• PathwayAndDataAnalysis / causalpath

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

  computational-biologybioinformaticsproteomicsphosphoproteomicscausality-analysispathway-analysispathways
  Language:Java 30

• Caleydo / pathfinder

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

  phoveaphovea-applicationpathfinderpathways
  Language:JavaScript 25

• decodebiology / geneSCF_inactive

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

  gene-set-clusteringenrichment-analysisgene-annotationgene-ontologykeggkegg-pathwaykegg-genepathwayspathway-analysisreactomefunctional-analysisreal-time-processingreal-time-analytics
  Language:Perl 20

• jdrudolph / photon

  PHOsphoproteomic dissecTiOn using Networks

  bioinformaticsbiological-data-analysisbiologypathwaysphosphoproteomicsphosphorylationproteomicssignaling-networkssignaling-pathways
  Language:Python 17

• PathwayMerger / PathMe

  Harmonizing pathway databases using Biological Expression Language (BEL)

  pathwayssystems-biologybioinformaticsbiological-expression-languagepathway-analysis
  Language:Python 17

• iVis-at-Bilkent / chise.js

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

  pathwayspathway-analysisnetwork-visualizationeditorbioinformaticssystems-biologybiologysbgn
  Language:JavaScript 15
• BioCor

  llrs / BioCor

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

  bioconductor-packagesbioinformaticsfunctional-similaritygenegene-setspathway-analysispathwayssimilaritysimilarity-measurement
  Language:R 14

• bio2bel / kegg

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

  pathwayssystems-biologynetworks-biologyproteinsbiological-expression-languagekegg
  Language:Python 13

• wikipathways / rWikiPathways

  R package for WikiPathways API

  bioinformaticsdata-accesspathwaysrpackage
  Language:HTML 13

• ComPath / ComPath

  A web application for exploring, analyzing, and curating pathway databases

  bioinformaticsbioinformatics-databasesgene-setspathway-analysispathwayssystems-biology
  Language:JavaScript 11

• dethebera / 100-days-of-Data-Science

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

  data-sciencepathwaysjourney
  Language:HTML 11

• greenelab / tad_pathways_pipeline

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

  gwascandidate-genestadanalysismethodologyworkflowpathwaystads
  Language:Python 11

• iVis-at-Bilkent / syblars

  SyBLaRS: Systems Biology Layout & Rendering Service

  systems-biologypathwayspathway-analysisnetwork-visualizationbioinformaticsgraphvizgraph-algorithmsgraph-drawing
  Language:JavaScript 11

• geneontology / noctua-models

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

  noctua-modelspathwaysgeneontologygo-camontologyannotation
  Language:Makefile 10

• nhsx / SynPath

  Proof Of Concept - Open Patient Pathway Generator using and an agent based approach

  nhspathwayssimulationsynthetic
  Language:Python 9

• ComPath / compath-resources

  This repository contains the different resources derived or generated using ComPath

  bioinformaticscurationjupyter-notebooksmappingspathway-analysispathwayssystem-biology
  Language:Jupyter Notebook 8

• geneontology / pathways2GO

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

  ontologygeneontologypathwaysgo-cambiopax
  Language:Java 8

• ps4dr / ps4dr

  Pathway Signatures for Drug Repositioning and Discovery

  drug-repurposingpathwaysbioinformaticsworkflowdrug-discoverymulti-modal-data
  Language:HTML 8

• awell-health / developer-hub

  Awell's Developer Hub website.

  graphqlhealthcareorchestrationpathwaysworkflows
  Language:TypeScript 7

• rosscm / fedup

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

  bioconductorenrichmentnetworkpathways
  Language:R 7

• PathwayAnalysisPlatform / PathwayMatcher_Dev

  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

  developmentproteoformspathwaysbiological-networksreactomepathway-analysis
  Language:Java 6

• bio2bel / reactome

  Integration of pathway-related information from Reactome in BEL

  pathwayssystem-biologynetworks-biologybiological-expression-languagereactome
  Language:Python 5

• geneontology / gocam-sif-pyexport

  Export GO-CAMs to SIF (Python)

  geneontologygo-camcytoscapeannotationspathways
  Language:Python 5

• PathwayMerger / PathMe-Viewer

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

  pathwaysvisualizationbioinformaticsnetworks-biologynetwork-visualizationpathway-analysis
  Language:JavaScript 5

• sales-lab / graphite

  GRAPH Interaction from pathway Topological Environment

  pathwayspathway-analysisbioinformaticsrmirror
  Language:R 5

• derhuerst / extract-gtfs-pathways

  Command-line tool to extract pathways from a GTFS dataset.

  gtfspathwaysaccessibilityclitransitpublic-transportgeojson
  Language:JavaScript 3

• TheVikJ / PHC-website

  The official Pathways Hack Club website

  hackclubhacktoberfesthacktoberfest2021pathways
  Language:JavaScript 3