Access to Biological Web Services from Python.

Python Client Package for WikiPathways

WikiPathways Database

The main web site for the WikiPathways project.

R package for pathway visualization

GPML2RDF converter

Mapping WikiPathways to chromosomes

Project to convert content of WPRDF into nanopublications.

Integration of pathway-related information from WikiPathways in BEL

Ready-to-use curated genesets for cinaR

Temporary repository of RDF of selected pathways from WikiPathways, supporting the Wikidata bot.

Queries for the WikiPathways SPARQL endpoint.

A compilation of pathway gene sets

Key Event enrichment of gene-expression data against molecular Adverse Outcome Pathways — Fisher/ORA and GSEA with FDR correction, interactive Cytoscape KE networks, batch cross-condition comparison and PDF reports. Consumes the molAOP Builder's mapping API.

Converts Reactome pathways to GPML format

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…

Bioclipse plugins for WikiPathways and PathVisio

WikiPathways Summit Planning

This ebook has information about life science databases, their SPARQL endpoints, what information they hold, what data models they use, and how to query those.

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