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

Language: Python - Size: 828 KB - Last synced at: 13 days ago - Pushed at: almost 5 years ago - Stars: 145 - Forks: 29

mahmoodlab/SurvPath

Modeling Dense Multimodal Interactions Between Biological Pathways and Histology for Survival Prediction - CVPR 2024

Language: Python - Size: 99.6 MB - Last synced at: 24 days ago - Pushed at: 5 months ago - Stars: 133 - Forks: 7

saezlab/OmnipathR

R client for the OmniPath web service

Language: R - Size: 36.6 MB - Last synced at: 24 days ago - Pushed at: about 1 month ago - Stars: 131 - Forks: 19

igordot/msigdbr

MSigDB gene sets for multiple organisms in a tidy data format

Language: R - Size: 77.4 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 74 - Forks: 14

Caleydo/caleydo 📦

Caleydo - Visualization for Molecular Biology

Language: Java - Size: 1.39 GB - Last synced at: 4 months ago - Pushed at: over 8 years ago - Stars: 58 - Forks: 14

iVis-at-Bilkent/pathway-mapper

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

Language: TypeScript - Size: 65.8 MB - Last synced at: 17 days ago - Pushed at: about 1 year ago - Stars: 57 - Forks: 27

iVis-at-Bilkent/newt

A web application to visualize and edit pathway models

Language: JavaScript - Size: 52.2 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 56 - Forks: 26

PathwayAndDataAnalysis/causalpath

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

Language: Java - Size: 12.6 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 41 - Forks: 11

JuliaOcean/AIBECS.jl

The ideal tool for exploring global marine biogeochemical cycles.

Language: Julia - Size: 371 MB - Last synced at: 7 days ago - Pushed at: 5 months ago - Stars: 38 - Forks: 7

geneontology/noctua

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

Language: JavaScript - Size: 192 MB - Last synced at: 22 days ago - Pushed at: over 1 year ago - Stars: 38 - Forks: 12

iVis-at-Bilkent/sbgnviz.js

A web based visualization tool for process description maps in SBGN

Language: JavaScript - Size: 120 MB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 35 - Forks: 13

Caleydo/pathfinder

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

Language: JavaScript - Size: 1.44 MB - Last synced at: 4 months ago - Pushed at: over 6 years ago - Stars: 26 - Forks: 8

decodebiology/geneSCF_inactive

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

Language: Perl - Size: 53.8 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 20 - Forks: 8

PathwayMerger/PathMe

Harmonizing pathway databases using Biological Expression Language (BEL)

Language: Python - Size: 698 KB - Last synced at: 24 days ago - Pushed at: 10 months ago - Stars: 19 - Forks: 2

wikipathways/rWikiPathways

R package for WikiPathways API

Language: HTML - Size: 9.13 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 17 - Forks: 6

jdrudolph/photon

PHOsphoproteomic dissecTiOn using Networks

Language: Python - Size: 55.6 MB - Last synced at: about 9 hours ago - Pushed at: over 4 years ago - Stars: 17 - Forks: 5

iVis-at-Bilkent/chise.js

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

Language: JavaScript - Size: 10.9 MB - Last synced at: 16 days ago - Pushed at: 3 months ago - Stars: 16 - Forks: 6

llrs/BioCor

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

Language: R - Size: 9.47 MB - Last synced at: 16 days ago - Pushed at: 4 months ago - Stars: 14 - Forks: 1

ComPath/ComPath

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

Language: JavaScript - Size: 28.6 MB - Last synced at: 20 days ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 0

bio2bel/kegg

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

Language: Python - Size: 297 KB - Last synced at: 17 days ago - Pushed at: about 3 years ago - Stars: 13 - Forks: 4

iVis-at-Bilkent/syblars

SyBLaRS: Systems Biology Layout & Rendering Service

Language: JavaScript - Size: 21.4 MB - Last synced at: 17 days ago - Pushed at: 5 months ago - Stars: 12 - Forks: 2

geneontology/noctua-models

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

Language: Makefile - Size: 6.62 GB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 11 - Forks: 3

onlythede/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.

Language: HTML - Size: 3.02 MB - Last synced at: 6 days ago - Pushed at: almost 4 years ago - Stars: 11 - Forks: 1

greenelab/tad_pathways_pipeline

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

Language: Python - Size: 2.24 MB - Last synced at: 20 days ago - Pushed at: over 5 years ago - Stars: 11 - Forks: 5

awell-health/developer-hub

Awell's Developer Hub website.

Language: TypeScript - Size: 9.73 MB - Last synced at: about 15 hours ago - Pushed at: about 16 hours ago - Stars: 10 - Forks: 10

geneontology/pathways2GO

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

Language: Java - Size: 39 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 10 - Forks: 0

nhsx/SynPath

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

Language: Python - Size: 2.23 MB - Last synced at: 11 months ago - Pushed at: about 2 years ago - Stars: 9 - Forks: 5

sales-lab/graphite

GRAPH Interaction from pathway Topological Environment

Language: R - Size: 33.5 MB - Last synced at: 18 days ago - Pushed at: 6 months ago - Stars: 8 - Forks: 2

ps4dr/ps4dr

Pathway Signatures for Drug Repositioning and Discovery

Language: HTML - Size: 400 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 2

ComPath/compath-resources

This repository contains the different resources derived or generated using ComPath

Language: Jupyter Notebook - Size: 3.58 MB - Last synced at: 12 months ago - Pushed at: almost 4 years ago - Stars: 8 - Forks: 1

rosscm/fedup

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

Language: R - Size: 10.8 MB - Last synced at: 7 days ago - Pushed at: almost 4 years ago - Stars: 7 - Forks: 0

PathwayMerger/PathMe-Viewer

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

Language: JavaScript - Size: 1.13 MB - Last synced at: 2 days ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 3

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

Language: Java - Size: 1.72 GB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 1

geneontology/gocam-sif-pyexport 📦

Export GO-CAMs to SIF (Python)

Language: Python - Size: 986 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 1

bio2bel/reactome

Integration of pathway-related information from Reactome in BEL

Language: Python - Size: 1.21 MB - Last synced at: 9 months ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 1

derhuerst/extract-gtfs-pathways

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

Language: JavaScript - Size: 57.6 KB - Last synced at: 7 days ago - Pushed at: 10 months ago - Stars: 4 - Forks: 0

hemekg/hemekg

Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders

Language: Python - Size: 2.32 MB - Last synced at: 9 days ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 3

arnaudporet/pathrider

Finding paths of interest in networks

Language: Go - Size: 2.3 MB - Last synced at: 10 months ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 2

TheVikJ/PHC-website

The official Pathways Hack Club website

Language: JavaScript - Size: 3.08 MB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 4

bio2bel/wikipathways

Integration of pathway-related information from WikiPathways in BEL

Language: Python - Size: 126 KB - Last synced at: 10 days ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 1

matveynator/chicha-isotope-map

Chicha Isotope Map — The Explorer of Invisible Roads. Radioactive isotope pathways. RadiaCode. AtomFAST. Written in GO.

Language: Go - Size: 38.2 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

wikipathways/nanopublications

Project to convert content of WPRDF into nanopublications.

Language: Java - Size: 43 KB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

JacopoRaffi/Pathways_Analysis

Computational Health Laboratory Project. Computer Science Master Degree University of Pisa. Academic Year 2022/2023

Language: R - Size: 1.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

PeltzLab-Stanford/mMap

Computational tool for prioritizing the genetic candidates based on the protein functional and regulatory features

Language: Python - Size: 7.38 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

arnaudporet/kgml2sif

Converting KGML encoded KEGG pathways to the SIF file format

Language: Python - Size: 2.96 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 2

ps4dr/results

Results of the manuscript

Language: HTML - Size: 175 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0

cannin/sbgn2sif Fork of arnaudporet/sbgn2sif

Converting SBGN-encoded pathways to the SIF file format

Language: Python - Size: 187 KB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1

arnaudporet/sbgn2sif

Converting SBGN encoded pathways to the SIF file format

Language: Python - Size: 185 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 2

kn-bibs/pathways-analysis

Testing, development environment for a new project of KN BIBS

Language: Python - Size: 147 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 10

dhimmel/pathways

A compilation of pathway gene sets

Language: Jupyter Notebook - Size: 2.38 MB - Last synced at: about 1 month ago - Pushed at: about 9 years ago - Stars: 2 - Forks: 3

geneontology/reactome-go-cams

A set of GO-CAMs built automatically from Reactome pathways.

Size: 150 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 1 - Forks: 0

reactome/fireworks-layout

Custom radial layout algorithm to visualise Reactome pathways in a space-filling graph

Language: Java - Size: 1.75 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 1 - Forks: 3

Alphawarrior21/AeroIntel

AeroIntel is a cutting-edge RAG based AI assistant chatbot-GPT powered by OpenAI & Pathway created to aid government policymakers and high officials, especially from the Center of Atmospheric Sciences. This application delivers detailed insights and data on air quality, pollution control initiatives.

Language: Python - Size: 13.2 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

DBRetina/DBRetina

DBRetina python package

Language: C++ - Size: 19.7 MB - Last synced at: 10 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 3

geneontology/unipathway

Unipathway ontology (inactive)

Language: Jinja - Size: 3.23 MB - Last synced at: 9 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

Bluestars1/BMI520-Autism-Genes

This repository is on Autism

Language: Jupyter Notebook - Size: 13.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

Edening/996.OUT.Pathways

Half-opinionated Half-reasonable Proposal for Getting Out of `996`

Size: 33.2 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

thierrygrimm/gene-expression-pca

Principal Component Analysis of mTOR Gene Expression data

Language: Jupyter Notebook - Size: 540 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

emiliesecherre/famat

Functional analysis of metabolic and transcriptomic data

Language: R - Size: 8.16 MB - Last synced at: 17 days ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

nhsx/SynPath_Diabetes

SynPath module for generating type 2 diabetes pathway

Language: Python - Size: 1.38 MB - Last synced at: 11 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 2

chiarabales/geneset_SV

Reference implementation of the paper Redundancy-aware unsupervised ranking based on game theory - application to gene enrichment analysis

Language: Python - Size: 119 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

StoneBelle/PersonalizedInvitations

Generated personalized invitations based on the different text files provided in path directory.

Language: Python - Size: 1.95 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

LuizCorrea-Dev/ListConversationCompose

projeto replicado do pathways do Developer.android com estudo de Jetpack-Compose

Language: Kotlin - Size: 98.6 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

geneontology/signor2gocam

Converting Signor pathways to GO-CAM

Language: Python - Size: 135 KB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 2

lvn3668/caBIO-load-scripts

ETL scripts to populate caBIO database

Size: 26.7 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

aasimayazwani/Machine-Learning-Aided-Retrosynthesis

Retrosynthesis has been used for a long time, but it's slower and prone to bias. Machine learning aided techniques like this can help speed up the process.

Language: HTML - Size: 416 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

bio2bel/go

A Bio2BEL package for converting the Gene Ontology (GO) to BEL

Language: Python - Size: 65.4 KB - Last synced at: 19 days ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

pathwayforte/reproducibility-survey

Evaluating the reprodubility of top-ranked publications

Language: Jupyter Notebook - Size: 1.54 MB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

PathwayMerger/PathMe-Resources

Resources derived from PathMe

Language: Jupyter Notebook - Size: 3.57 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

geneontology/activity-flow-editor

Lightweight reusable web component for activity-centric visualizations and edits

Size: 3.91 KB - Last synced at: 9 months ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

imwiththou/PathwayNet

PathwayNet is a project based on Python and Bioinformatics. It tries to build up mathematic modes on simulating pathways of amino acid synthesis in E. coli.

Language: Python - Size: 201 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

gari3008ma/RNA-seq

colorectal cancer

Size: 10.7 KB - Last synced at: 3 months ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 1

Cytogence/rnaSQLite

Set of tools to organize pathway, RNAseq, and annotation data for subsequent analysis.

Language: Perl - Size: 36.1 KB - Last synced at: 9 months ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

PathVisio/FindYourInteraction

PathVisio plugin to find relevant metabolic reactions from Rhea

Language: Java - Size: 13.7 KB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 1

temichelle13/actions-learning-pathway

✅ Completed: Learning pathway for automation and GitHub actions

Language: CSS - Size: 39.1 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

iVis-at-Bilkent/sybvals

SyBValS: Systems Biology Validation Service

Language: JavaScript - Size: 2.34 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

parthosen/parthosen.github.io

My personal website

Language: HTML - Size: 10.4 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1

kinzaR/signor2Hipathia

In this project, we aim to integrate pathways from the Signor database to make them compatible with the Hipathia method. Here is an overview of the project and instructions for running the main R script.

Language: HTML - Size: 12.6 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

geneontology/go-pombase

Code for generating process-centric GO-CAM models from GAFs

Language: Python - Size: 84 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

marinoandrea/stargate-x

Python implementation of a bipartite directed multigraph extracted from the Reactome biological pathway database.

Language: Python - Size: 67.8 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

jgo28/BioPath

Web Application Tool for Learning BioChemistry

Language: CSS - Size: 4.92 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ol-th/pathlink

Final-year project: System for aggregation and structured querying of cancer pathway data

Language: Python - Size: 295 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

geneontology/gocamgen

Base repo for constructing GO-CAM model RDF

Language: Python - Size: 295 KB - Last synced at: 7 days ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

RuchaBhattJoshi/ComposePathways

this is a sample app following jetpack pathways.

Language: Kotlin - Size: 1.42 MB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

larsgw/gpml-rhea

Collect chemical reactions from a GPML file and look for matching Rhea equations.

Language: JavaScript - Size: 31.3 KB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1

pouryany/CentralityInPathways

Language: R - Size: 190 MB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

kkmann/pwcuratr

Curate gene pathway clusters using functional interactions

Language: R - Size: 68.7 MB - Last synced at: 3 days ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

greenelab/netscape

Exploring the network/pathway regularization landscape for gene expression data

Language: Jupyter Notebook - Size: 6.09 MB - Last synced at: about 2 months ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1

gualapuromoises/pathwaysKEGG

Extract pathways from KEGG database using EC entries.

Language: R - Size: 1.48 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

andrawaag/pathway_interaction_models

Language: Python - Size: 21.5 KB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 1

frederikprijck/angular-escher

An Angular application integrating escher for visualizing biological pathways.

Language: TypeScript - Size: 74.2 KB - Last synced at: about 1 month ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0