Function heatmap2 is revised based on the heatmap.2 function in package gplot. Secondary functions colorpanel, greenred, invalid and odd are identical to the version in gplots. gs.heatmap is a wrapper function of heatmap2 to visualize whole gene set perturbations.
Function vennDiagram2 is a revised form of function vennDiagram from package limma. Associated function vennCounts is identical to the version in limma.
Function kegg.species.code is identical to the version in pathview.
Functions deComp and rownorm were written by Weijun Luo, the author of gage package.