adds vignette, deletes old files
proper docs for bg dataset
updates README so it (mostly) matches the vignette
stattest updates (new library size adjustment, better docs, etc)
bg.rda saved with right compression
fixes clusterTranscripts docs
updates .Rbuildignore and .gitignore
only imports lmFit from limma
fixes dependencies (adds knitr/knitcitations for vignette, deletes reshape, only imports lmFit from limma)
fixes IRanges/S4Vectors Rle import issue;
fixes gexpr method
overhauls collapseTranscripts