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)