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dvklopfenstein /ReactomePy

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

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

UpdatedOct 12, 2024
Python

moosa-r /rbioapi

rbioapi: User-Friendly R Interface to Biologic Web Services' API

cran bioinformatics enrichment r string biology api-client rstats uniprot reactome enrichment-analysis jaspar panther enrichr over-representation-analysis rstats-package mieaa

UpdatedFeb 3, 2025
R

decodebiology /geneSCF_inactive

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

UpdatedOct 30, 2020
Perl

cwieder /PathIntegrate

PathIntegrate Python package for pathway-based multi-omics data integration

sklearn metabolomics pathway-analysis reactome multi-omics-integration

UpdatedNov 9, 2024
Jupyter Notebook

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

development pathways pathway-analysis reactome biological-networks proteoforms

UpdatedMar 4, 2019
Java

linas /biome-distribution

Research into statistical distributions of genomes, proteomes and reactomes

proteomics reactome genomic-data-analysis genomics-visualization proteogenomics reactome-pathway

UpdatedFeb 14, 2022
Scheme

bio2bel /reactome

Integration of pathway-related information from Reactome in BEL

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

UpdatedNov 18, 2020
Python

santo-it /reactome-orientdb

OrientDB graph database version of the Reactome Database

orientdb reactome

UpdatedJul 8, 2017

RichardMatzko /BioNexusSentinel

A research biochemical network explorer and genetic cytohistological encyclopedia.

rna-seq genetics synthetic-biology systems-biology gene-expression reactome reaction-networks

UpdatedApr 4, 2024
Python

dhimmel /pathways

A compilation of pathway gene sets

tsv human rephetio hetionet genes pathways wikipathways reactome pathway-interaction-database pathway-commons

UpdatedApr 2, 2016
Jupyter Notebook

cannin /sbgn2sif

Converting SBGN-encoded pathways to the SIF file format

pathways kegg reactome sbgn biological-networks sif sbgnml sbgn2sif sbgn-to-sif

UpdatedMay 8, 2020
Python

francescopatane96 /RNA-seq_Pipeline

Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last…

bam-files rna-seq r script deseq2 rna-seq-analysis kegg wikipathways reactome ora geneontology gsea rna-seq-pipeline reactome-pathway differentially-expressed-genes clusterprofiler deseq2-analysis gene-set-enrichment-analysis diseaseontology over-rapresentation-analysis

UpdatedApr 14, 2023
Jupyter Notebook

wikipathways /reactome2gpml-converter

Converts Reactome pathways to GPML format

wikipathways reactome pathway gpml

UpdatedMar 30, 2023
Java

arnaudporet /sbgn2sif

Converting SBGN encoded pathways to the SIF file format

converter signaling-pathways pathways reactome sbgn biological-networks sif sbgnml sbgn-ml sif-file-format reactome-pathways sbgn-file-format sbgn2sif sbgn-to-sif

UpdatedApr 22, 2020
Python

aprezvykh /bioinformatics

some scripts to process transcriptomics and Chip-seq data

r rnaseq deseq2 reactome edger gage gsea pathview topgo

UpdatedMay 10, 2019
R

geneontology /reactome-go-cams

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

pathways reactome geneontology reactome-pathway noctua-models go-cam

UpdatedNov 5, 2024

Caleydo /pathfinder_graph_reactome

pathfinderhttp://reactome.org/ graph binding

pathfinder phovea phovea-server-plugin reactome

UpdatedJun 28, 2017
Python

EBI-EMBL-Bioinformatics-tools /Bardet-Biedl-Syndrome

BBS Project developed by Ronald Pardo, Ana Sofia Villa and Gabriela Moreno for the course of EBI tools @ Universidad de los Andes 2024-02.

jupyter-notebook computational-biology ensemble uniprot reactome ebi alphafold

UpdatedNov 9, 2024
Jupyter Notebook

pasculorente /diagram-exporter-example

An example on how to use reactome Rest API

pathway-analysis reactome diagram-exporter

UpdatedDec 4, 2017
Jupyter Notebook

pratiklodha /graphql

Google Summer Of Code 2020.

javascript graphql neo4j-database reactome

UpdatedAug 13, 2020
JavaScript

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