riverplot — tool to generate sankey diagrams. Blog post, package on CRAN
pca3d — tool to visualise principal component analysis. Blog post, package on CRAN
tagcloud — creating tag clouds in R. Blog post, package on CRAN
tmod — gene set enrichment analysis. Package on CRAN
myfuncs — collection of bits and pieces. Blog post, package on Copy.to
log Fold Change 
Could you teach me how to use tmod package in the analysis of Arabidopsis thaliana mircoarray data.
Hi sun, send me an e-mail (use the package maintainer field in the CRAN package).
In general, tmod only contains predefined gene sets for humans, so you need to (i) obtain gene sets and (ii) make them usable by tmod. The (ii) is super easy once you have the gene sets. The (i) is the real problem here.
Using google, I found the following web site: http://structuralbiology.cau.edu.cn/PlantGSEA — this seems like a nice resource to start with. You can download the gene sets (see downloads page) and, if you contact me, I can help you to load these modules into tmod.
I have sent email to you.