For documentation, see the wiki.
News:
2011.06.27: split-pcl for interactive splitting of PCL files
2011.06.29: .java files are in edu/princeton/function/tools, and
.class files are placed in the same directory
2011.07.18: SeriesFamilyParser.java now counts certain lines with terminating tabs toward missing value count
2011.07.19: Pipeline now supports per-platform family.soft files (GSEnnnGPLmmm_family.soft)
2011.07.31: The following are now supported:
* splitting of GSE files by platform (split-gse-by-platform);
* analysis of sample overlaps amongst GSE files (analyzeGSMs);
* automated excision of samples from GSE files based on analysis results (analyzeGSMs --proceed)