Conditional BED output in edgeR.
Moved DESeq and bed-utils.R to R2.15
Changed the visible names of convert-x-bam-to-edger.R scripts and
updated the manual.
Updated edgeR multivariate to BioC2.11
Updates tools-ngs.html
Updates to manuals.
edgeR classic: modified filtering based on counts, removed fixed
prior.n, added trended dispersion
edgeR glm, moved filtering and resizing before normalization
Chromosomal coord printing added to HTSeq-count
Merge branch 'master' into htseq-chr
HTSeq modified so that it prints coordinates