It is my hope that this directory of code, reference materials, and raw data will provide a self-sufficient archive of what the data means, how to interpret it, and how to repeat it. In order to get maximum benefit from it, a few pieces should be noted.
This is a mix of bash, perl, R, python, ruby, excel, and whatever other random tools I find at hand. I have collected the source code for some of the relevant tools in src/. Thus it should be possible (given a complete toolchain) to compile everything necessary. The R environment I use for this code is set up in the Rprofile. It calls libraries, these may be installed with the bioconductor commands in the .Rprofile, or by running [R_setup.R].
The html documents which make up the (hopefully) interesting part of this tree are generated via knitr, which is a wonderful tool for self-documenting code. The actual documents I write on are the .rmd files. When ready to publish some new changes, I save the changes to the .rmd files and run make(1) from the toplevel directory.