Access to Biological Web Services from Python.

Python Client Package for WikiPathways

WikiPathways Database

The main web site for the WikiPathways project.

GPML2RDF converter

Project to convert content of WPRDF into nanopublications.

Integration of pathway-related information from WikiPathways in BEL

Mapping WikiPathways to chromosomes

Ready-to-use curated genesets for cinaR

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

A compilation of pathway gene sets

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...

Queries for the WikiPathways SPARQL endpoint.

WikiPathways Summit Planning

Converts Reactome pathways to GPML format

Bioclipse plugins for WikiPathways and PathVisio

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

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.

WikiPathways SPARQL Book

#metawinterschool contribution by BiGCaT

Repository for code to create the Europe PMC external links

OpenAPI to extract information from WikiPathways.

KNIME nodes for WikiPathways.

R package for pathway visualization