YuLab-SMU/enrichplot

Visualization of Functional Enrichment Result

Language: R - Size: 658 KB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 216 - Forks: 61

willgryan/PAVER

PAVER: Pathway Analysis Visualization with Embedding Representations

Language: R - Size: 745 KB - Last synced: about 22 hours ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

jackbibby1/SCPA

R package for pathway analysis in scRNA-seq data

Language: R - Size: 41.2 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 53 - Forks: 4

noobCoding/CellEnrich Fork of unistbig/CellEnrich

Pathway enrichment analysis / visualize for Single Cell Data

Language: R - Size: 363 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0

markziemann/mitch_legacy

An R package for multi-dimensional pathway enrichment analysis (legacy repo)

Language: R - Size: 78.5 MB - Last synced: 7 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

markziemann/mitch

An R package for multi-dimensional pathway enrichment analysis

Language: R - Size: 9.44 MB - Last synced: 7 days ago - Pushed: 13 days ago - Stars: 14 - Forks: 4

shawlab-moffitt/PATH-SURVEYOR-Suite

Survival Analysis through the integration of expression data, phenotype data, and clinical data

Language: R - Size: 596 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

federicomarini/GeneTonic

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

Language: R - Size: 115 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 75 - Forks: 8

sykhro/cancol-analysis 📦

Language: Jupyter Notebook - Size: 41.3 MB - Last synced: 15 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

sales-lab/graphite

GRAPH Interaction from pathway Topological Environment

Language: R - Size: 33.5 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 5 - Forks: 2

meringlab/annotation_system_assessment

Snakemake pipeline to benchmark 11 functional pathway annotation systems

Language: Python - Size: 7.1 MB - Last synced: 22 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

llrs/BioCor

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

Language: R - Size: 8.3 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 14 - Forks: 1

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.

Language: Python - Size: 264 MB - Last synced: 27 days ago - Pushed: almost 2 years ago - Stars: 91 - Forks: 28

iiasa/ipcc_sr15_scenario_analysis

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

Language: Jupyter Notebook - Size: 386 KB - Last synced: about 7 hours ago - Pushed: over 3 years ago - Stars: 64 - Forks: 30

futianfan/GenoCraft

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

Language: SCSS - Size: 68.2 MB - Last synced: 15 days ago - Pushed: 28 days ago - Stars: 13 - Forks: 0

OICR/mp-biopath

Mathematical Programming tool for inferring node values in perturbed biological pathways.

Language: Julia - Size: 4.31 MB - Last synced: 30 days ago - Pushed: 30 days ago - Stars: 4 - Forks: 0

LucasESBS/vega

VEGA: VAE Enhanced by Gene Annotations

Language: Python - Size: 26.1 MB - Last synced: 7 days ago - Pushed: about 2 years ago - Stars: 13 - Forks: 2

BaderLab/POPPATHR

Population-based pathway analysis of SNP-SNP coevolution

Language: R - Size: 14.1 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

igordot/msigdbr

MSigDB gene sets for multiple organisms in a tidy data format

Language: R - Size: 62.3 MB - Last synced: 13 days ago - Pushed: about 1 year ago - Stars: 64 - Forks: 12

cxli233/ggpathway

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

Size: 385 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 46 - Forks: 4

DecoPath/DecoPath

A web application for visualizing and exploring the consensus across pathway enrichment results

Language: Python - Size: 27.1 MB - Last synced: 2 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 1

malhamdoosh/EGSEA

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.

Language: R - Size: 5.6 MB - Last synced: 2 months ago - Pushed: 4 months ago - Stars: 9 - Forks: 4

cwieder/py-ssPA

Single sample pathway analysis tools for omics data

Language: Jupyter Notebook - Size: 8.05 MB - Last synced: 10 days ago - Pushed: about 2 months ago - Stars: 9 - Forks: 4

lemaslab/rump

A Reproducible Untargeted Metabolomics Data Processing Pipeline

Language: HTML - Size: 2.76 GB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 10 - Forks: 8

wikipathways/summit2018

WikiPathways Summit Planning

Size: 2.93 KB - Last synced: 7 days ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

iVis-at-Bilkent/newt

A web application to visualize and edit pathway models

Language: JavaScript - Size: 43 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 50 - Forks: 26

krassowski/gsea-api

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

Language: Python - Size: 162 KB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 14 - Forks: 2

ComPath/ComPath

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

Language: JavaScript - Size: 28.6 MB - Last synced: 2 days ago - Pushed: 9 months ago - Stars: 11 - Forks: 0

knowmics-lab/RNAdetector

RNAdetector: a free user-friendly and stand-alone software for RNA-Seq data analysis

Language: JavaScript - Size: 73.6 MB - Last synced: about 19 hours ago - Pushed: 1 day ago - Stars: 8 - Forks: 8

PathwayAndDataAnalysis/causalpath

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

Language: Java - Size: 12.6 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 30 - Forks: 10

pathwayforte/pathway-forte

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

Language: Python - Size: 2.13 MB - Last synced: 15 days ago - Pushed: about 3 years ago - Stars: 13 - Forks: 6

reactome/reactome2py

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

Language: Python - Size: 337 KB - Last synced: 30 days ago - Pushed: 4 months ago - Stars: 25 - Forks: 10

bio2bel/msig

Integration of pathway-related information from MSigDB in BEL

Language: Python - Size: 66.4 KB - Last synced: 3 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

iVis-at-Bilkent/syblars

SyBLaRS: Systems Biology Layout & Rendering Service

Language: JavaScript - Size: 21.4 MB - Last synced: 22 days ago - Pushed: about 1 year ago - Stars: 11 - Forks: 1

iVis-at-Bilkent/pathway-mapper

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

Language: TypeScript - Size: 65.8 MB - Last synced: 22 days ago - Pushed: about 2 months ago - Stars: 55 - Forks: 28

dvklopfenstein/ReactomePy

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

Language: Python - Size: 17.3 MB - Last synced: 15 days ago - Pushed: 6 months ago - Stars: 21 - Forks: 4

arnaudporet/pathrider

Finding paths of interest in networks

Language: Go - Size: 2.3 MB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 3 - Forks: 2

eriklarsen4/RNAseq

Template R code for bioinformatics analysis pipeline of transcriptomic Illumina datasets

Language: HTML - Size: 14 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

CCBR/MAAPster

MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data

Language: R - Size: 50.5 MB - Last synced: 28 days ago - Pushed: 4 months ago - Stars: 9 - Forks: 6

iVis-at-Bilkent/chise.js

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

Language: JavaScript - Size: 10.3 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 15 - Forks: 5

mcrewcow/RGC_Dnmt3a_pONC2d_paper

Retinal ganglion cells regeneration in 2 days post optic nerve crush retina | Lydia Tai | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

Language: R - Size: 84 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 1

elixir-luxembourg/BH2020-galaxy-dpmaps

A github repo for the BioHackathon Europe 2020 "An interface between Galaxy and disease/pathway maps"

Language: JavaScript - Size: 171 KB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

CBFLivUni/SkeletalVis-Transcriptomics

Nextflow pipeline for microarray and RNA-seq

Language: R - Size: 11.6 MB - Last synced: 6 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

PathwayMerger/PathMe

Harmonizing pathway databases using Biological Expression Language (BEL)

Language: Python - Size: 691 KB - Last synced: about 19 hours ago - Pushed: 8 months ago - Stars: 17 - Forks: 2

mims-harvard/pathways

Disease pathways in the human interactome

Language: Python - Size: 1.46 MB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 21 - Forks: 6

raeslab/GMMs

A manually curated database of human gut metabolic modules.

Size: 13.7 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 14 - Forks: 5

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: 7 months ago - Pushed: about 5 years ago - Stars: 6 - Forks: 1

omixer/omixer-rpmR

An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles

Language: R - Size: 2.99 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 9 - Forks: 5

hagax8/PathAnalyzor

Just another wrapper for pathway analysis using MAGMA

Language: Shell - Size: 28.4 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0

greenelab/GEA_Community_Detection

Overrepresentation analysis for KEGG and PID pathways using community detection

Language: Python - Size: 5 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 7 - Forks: 6

mjr129/metaboclust

█ 𝐓𝐇𝐈𝐒 𝐈𝐒 𝐀 𝐌𝐈𝐑𝐑𝐎𝐑 𝐎𝐅 𝐓𝐇𝐄 𝐒𝐀𝐌𝐄 𝐑𝐄𝐏𝐎𝐒𝐈𝐓𝐎𝐑𝐘 𝐎𝐍 𝐁𝐈𝐓𝐁𝐔𝐂𝐊𝐄𝐓 – 𝐓𝐇𝐈𝐒 𝐏𝐀𝐆𝐄 𝐈𝐒 𝐍𝐎𝐓 𝐌𝐎𝐍𝐈𝐓𝐎𝐑𝐄𝐃 – 𝐏𝐋𝐄𝐀𝐒𝐄 𝐒𝐄𝐄 𝐓𝐇𝐄 𝐁𝐈𝐓𝐁𝐔𝐂𝐊𝐄𝐓 𝐏𝐀𝐆𝐄 𝐅𝐎𝐑 𝐓𝐇𝐄 𝐋𝐀𝐓𝐄𝐒𝐓 𝐃𝐄𝐓𝐀𝐈𝐋𝐒

Language: C# - Size: 7.95 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 3 - Forks: 2

kn-bibs/pathways-analysis

Testing, development environment for a new project of KN BIBS

Language: Python - Size: 147 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 10

raeslab/omixer-rpm

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

Language: Java - Size: 112 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 23 - Forks: 7

NKI-CCB/flexgsea-r

Flexible gene set enrichment analysis

Language: R - Size: 90.8 KB - Last synced: 3 days ago - Pushed: over 2 years ago - Stars: 10 - Forks: 2

qbic-pipelines/rnadeseq

Differential gene expression analysis and pathway analysis of RNAseq data

Language: Nextflow - Size: 62.6 MB - Last synced: about 6 hours ago - Pushed: about 7 hours ago - Stars: 32 - Forks: 20

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.

Language: Jupyter Notebook - Size: 136 MB - Last synced: 9 months ago - Pushed: almost 6 years ago - Stars: 7 - Forks: 2

llrs/pathways-study

Analyze and compare different pathway resources

Language: R - Size: 4.88 KB - Last synced: 9 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

llrs/GSEAdv 📦

Package to analyse gene sets

Language: R - Size: 500 KB - Last synced: 9 months ago - Pushed: over 5 years ago - Stars: 5 - Forks: 1

pasculorente/diagram-exporter-example

An example on how to use reactome Rest API

Language: Jupyter Notebook - Size: 2.91 MB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

pasculorente/diagram-exporter Fork of reactome-pwp/diagram-exporter 📦

Exporter of the diagram layout to different formats

Language: Java - Size: 10.5 MB - Last synced: 9 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

AlexsLemonade/refinebio-examples

Example workflows for refine.bio data

Language: HTML - Size: 773 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 10 - Forks: 5

decodebiology/geneSCF_inactive

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

Language: Perl - Size: 53.8 MB - Last synced: 5 months ago - Pushed: over 3 years ago - Stars: 20 - Forks: 8

albertme0308/GSApp

GSApp Pathway Analysis

Language: HTML - Size: 10.2 MB - Last synced: 4 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

ComPath/compath-resources

This repository contains the different resources derived or generated using ComPath

Language: Jupyter Notebook - Size: 3.58 MB - Last synced: 15 days ago - Pushed: almost 3 years ago - Stars: 8 - Forks: 1

Micromeda/pygenprop

A python library for programmatic usage of EBI InterPro Genome Properties.

Language: Python - Size: 4.52 MB - Last synced: 9 days ago - Pushed: about 1 year ago - Stars: 9 - Forks: 4

collaborativebioinformatics/Disease_subsetting

Colorectal cancer CMs subtyping and personalized medication recommendation based on RNA seq pathway analysis

Language: Jupyter Notebook - Size: 761 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 8 - Forks: 2

ComPath/ComPath-Utils 📦

A repository containing abstract classes that Bio2BEL repos should extend to be adapted to the Compath environment

Size: 75.2 KB - Last synced: 15 days ago - Pushed: about 4 years ago - Stars: 0 - 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: 15 days ago - Pushed: over 4 years ago - Stars: 5 - Forks: 3

nedaghohabi/Colorectal_Cancer_Subsetting Fork of collaborativebioinformatics/Disease_subsetting

Colorectal cancer CMSs subtyping and personalized medication recommendation based on RNA seq pathway analysis

Language: Jupyter Notebook - Size: 651 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

shawlab-moffitt/DRPPM-PATH-SURVEIOR

Survival Analysis through the integration of expression data, phenotype data, and clinical data

Language: R - Size: 392 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

santurini/DAG-Linkage-Analysis-in-R

Implementing the Linkage and Pathway Universal Tests using the clrdag package for Direceted Acyclic Graphs. Testing the two tests on cytometry data to analyze the links.

Language: HTML - Size: 947 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

niaid/pathways

Training materials related to pathways data analysis

Size: 2.93 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

hancockinformatics/clusterPathways

Use Jaccard index and constituent genes to identify groups of similar pathways

Language: R - Size: 1.06 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

draeger-lab/InCroMAP

Integrated analysis of Cross-platform MicroArray and Pathway data

Language: Java - Size: 382 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 2

hallamlab/chap

CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)

Language: Python - Size: 354 KB - Last synced: 17 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

CoXPath/CoXPath

Scripts and data from "Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms"

Language: Jupyter Notebook - Size: 49.2 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 4

genepattern/CellFie

Language: HTML - Size: 3.54 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 2

pathwayforte/results

Results of the evaluation of pathway databases using TCGA datasets

Language: Jupyter Notebook - Size: 13.5 MB - Last synced: 15 days ago - Pushed: about 4 years ago - Stars: 6 - Forks: 0

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

Language: Rich Text Format - Size: 415 KB - Last synced: about 2 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 6

alaimos/mithril-standalone

This repository hosts the java implementation of MITHrIL and SPECIFIC

Language: Java - Size: 223 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

alaimos/SPECifIC

SPECifIC - Sub-Pathway ExtraCtor and enrICher

Language: JavaScript - Size: 34.5 MB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0

SteveLane/hierarch-path

Investigating the use of hierarchical modelling for pathway analyses

Language: R - Size: 51.8 KB - Last synced: 28 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

ComPath/ComPath-HGNC

A wrapper around Bio2BEL HGNC for ComPath

Language: Python - Size: 32.2 KB - Last synced: 15 days ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

gloriachin/PathwayEenrichmentAnalysis

Language: Python - Size: 3.91 KB - Last synced: 12 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

egonw/knime-wikipathways

KNIME nodes for WikiPathways.

Language: Java - Size: 46.9 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0