23 results for “topic:reactome”
Explore biomolecular pathways in Reactome from the command-line or a Python script
rbioapi: User-Friendly R Interface to Biologic Web Services' API
GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF
PathIntegrate Python package for pathway-based multi-omics data integration
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
Research into statistical distributions of genomes, proteomes and reactomes
Integration of pathway-related information from Reactome in BEL
OrientDB graph database version of the Reactome Database
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...
Converting SBGN encoded pathways to the SIF file format
A compilation of pathway gene sets
A research biochemical network explorer and genetic cytohistological encyclopedia.
Converts Reactome pathways to GPML format
some scripts to process transcriptomics and Chip-seq data
A set of GO-CAMs built automatically from Reactome pathways.
BBS Project developed by Ronald Pardo, Ana Sofia Villa and Gabriela Moreno for the course of EBI tools @ Universidad de los Andes 2024-02.
pathfinder http://reactome.org/ graph binding
Downstream Analysis of RNA-Seq Results in R: GSEA, PPI Networks, and Biological Interpretation
An AnyWidget component for interactive embedding of Reactome Pathway browsers
An example on how to use reactome Rest API
Curate gene pathway clusters using functional interactions
Python implementation of a bipartite directed multigraph extracted from the Reactome biological pathway database.
pipeline for TMT/LFQ proteomics: QC, volcano plots, and Reactome enrichment