reactome

There are 1 repository under reactome topic.

• dvklopfenstein / ReactomePy

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

  reactomereactome-pathwaybiological-networksmolecular-biologypathway-enrichment-analysispathway-analysisbiotechnologybiotechbioinformaticsbioinformatics-pipelinebioinformatics-analysisbioinformatics-scriptsbioinformatics-toolpathway-modelsprotein-protein-interaction
  Language:Python 24

• moosa-r / rbioapi

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

  api-clientbioinformaticsbiologycranenrichment-analysisrrstatsrstats-packagejasparover-representation-analysispantherreactomemieaaenrichrstringuniprotenrichment
  Language:R 22

• 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

• cwieder / PathIntegrate

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

  metabolomicsmulti-omics-integrationpathway-analysisreactomesklearn
  Language:Jupyter Notebook 16

• 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 7

• linas / biome-distribution

  Research into statistical distributions of genomes, proteomes and reactomes

  genomic-data-analysisgenomics-visualizationproteomicsproteogenomicsreactomereactome-pathway
  Language:Scheme 6

• bio2bel / reactome

  Integration of pathway-related information from Reactome in BEL

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

• santo-it / reactome-orientdb

  OrientDB graph database version of the Reactome Database

  orientdbreactome
  3

• arnaudporet / sbgn2sif

  Converting SBGN encoded pathways to the SIF file format

  biological-networksconverterpathwaysreactomereactome-pathwayssbgnsbgn-file-formatsbgn-mlsbgn-to-sifsbgn2sifsbgnmlsifsif-file-formatsignaling-pathways
  Language:Python 2

• cannin / sbgn2sif

  Converting SBGN-encoded pathways to the SIF file format

  biological-networkskeggpathwaysreactomesbgnsbgn-to-sifsbgn2sifsbgnmlsif
  Language:Python 2

• dhimmel / pathways

  A compilation of pathway gene sets

  pathwayshumangeneswikipathwaysreactomepathway-interaction-databasepathway-commonstsvrephetiohetionet
  Language:Jupyter Notebook 2

• 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 module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...

  bam-filesclusterprofilerdeseq2deseq2-analysisdifferentially-expressed-genesgene-set-enrichment-analysisgeneontologygseakeggorarreactomereactome-pathwayrna-seqrna-seq-analysisrna-seq-pipelinescriptwikipathwaysdiseaseontologyover-rapresentation-analysis
  Language:Jupyter Notebook 2

• RichardMatzko / BioNexusSentinel

  A research biochemical network explorer and genetic cytohistological encyclopedia.

  gene-expressiongeneticsreaction-networksreactomesynthetic-biologysystems-biologyrna-seq
  Language:Python 2

• wikipathways / reactome2gpml-converter

  Converts Reactome pathways to GPML format

  reactomepathwaywikipathwaysgpml
  Language:Java 2

• aprezvykh / bioinformatics

  some scripts to process transcriptomics and Chip-seq data

  rrnaseqgseaedgertopgodeseq2gagereactomepathview
  Language:R 1

• geneontology / reactome-go-cams

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

  geneontologygo-camnoctua-modelspathwaysreactomereactome-pathway
  1

• 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.

  alphafoldcomputational-biologyebiensemblejupyter-notebookreactomeuniprot
  Language:Jupyter Notebook 0

• marinoandrea / stargate-x

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

  reactomegraphbiologypathwayspathwaybipartitereactome-graphreactome-database
  Language:Python 0

• merlinis12 / Downstream-Analysis-of-RNA-Seq-Results

  Downstream Analysis of RNA-Seq Results in R: GSEA, PPI Networks, and Biological Interpretation

  drug-repurposinggo-pathwaygseakeggppi-networksreactome
  Language:HTML 0

• pasculorente / diagram-exporter

  Exporter of the diagram layout to different formats

  reactomejpgpngneo4jdiagrampathpathway-analysis
  Language:Java 0

• pasculorente / diagram-exporter-example

  An example on how to use reactome Rest API

  reactomediagram-exporterpathway-analysis
  Language:Jupyter Notebook 0

• pasculorente / fireworks-exporter

  Service to generate images of top level pathway view (the fireworks).

  reactome
  Language:Java 0

• Caleydo / pathfinder_graph_reactome

  pathfinder http://reactome.org/ graph binding

  phoveaphovea-server-pluginpathfinderreactome
  Language:Python

• kkmann / pwcuratr

  Curate gene pathway clusters using functional interactions

  pathwaysreactomecuration
  Language:R

• nursa-reactome / gsea-desktop

  This fork is intended solely for generating a GSEA jar file that is compatible with Reactome.

  reactome
  Language:Java

• pratiklodha / graphql

  Google Summer Of Code 2020.

  reactomegraphqlneo4j-databasejavascript
  Language:JavaScript

• riyavsinha / reactome-anywidget

  An AnyWidget component for interactive embedding of Reactome Pathway browsers

  anywidgetbioinformaticsreactome
  Language:Python