[BioC] Pathview and GAGE now work with essentially all KEGG species

[Luo Weijun]

Pathview now work with essentially all KEGG species (about 2300 to date and more forthcoming). This is important for studies on none model organisms or rare species. In the meantime, Pathview also supported KEGG Orthology (with species="ko"). This makes pathway analysis and visualization feasible with non-KEGG species or metagenomics/microbiome data. Please check Subsection 7.5 in the vignette for details. 

A new function, kegg.gsets, has been introduced in the gage package. You may use it to compile pathway gene set data any time needed for one of the 2300 KEGG species and KEGG Orthology (with species="ko"). In addition, you get the most updated pathway gene set data as it is retrieved from KEGG in real time. Please check the help info on the function for details.

These features are available with the latest release of gage and pathview packages, and you need to work with BioC 2.13 (current release version) or newer version:
http://bioconductor.org/packages/release/bioc/html/gage.html
http://bioconductor.org/packages/release/bioc/html/pathview.html