R Onto-Tools suite iPathwayGuide

From iPathwayGuide, our pathway analysis approach is based on novel Impact Analysis method. This paper, published in Genome Research, explains the underlying analytic method and also demonstrates how Impact Analysis avoids costly false positive results as generated by other methods such as Over-Representation Analysis. The tool is also available from ROntoTools

advanced r wiki

From hadley, who is like a god in R.
The discussion of environment is really helpful. I am aware of other excellent resources, but still did not get it from there. 

graphic output for non-pdf file under unix without X11

bitmap('convergence%03d.png', height=11, width=8, res=600);
plot(post[, selectNode2Plot])
dev.off();

Created by Pretty R at inside-R.org

sas datasets IO with R

R code lines below are run without SAS installed.