Search code examples
rpackagecell

Does anyone know how to retrieve list of cell cycle genes from KEGG in R?


I know how to retrieve a list of genes for specific pathways from KEGG website by using KEGG API but I couldn't find any packages that could do the same thing in R. The only annotation package I found was KEGG.db which just give a list of available pathways in KEGG.

http://www.kegg.jp/kegg/docs/keggapi.html

by entering the pathway ID and search it on KEGG like this one for cell cycle genes:

http://rest.kegg.jp/get/hsa04110

Does anybody know any package in R/solution that could help me out with my problem?

Thanks in advance,


Solution

  • After rereading your question, I believe this the R package that can help you. It is on bioconductor and allows you to interact through R and REST with KEGG.

    KEGGREST

    KEGGREST: Client-side REST access to KEGG

    A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.