bug fix in the tophat2 index path.
miRNA up-down tool and manual updated.
Updated Copy number analysis tutorial.
Embster new version page removed.
DESeq manual updated.
DESeq manual.
Trimmomatic polish.
VM front page updated.
Mac instructions added to VM front page.
Preprocessing tools reorganized in XML.
eXpress manual and fixes to the tool.
RSeQC: added inner distance plot
Tophat2: added parameters (--no-mixe, --no-discordant), updated manual
Tophat2 with index building
Merge branch 'master' of https://github.com/chipster/chipster.git
tophat2
Tophat2 with index building manual pages
Added reference to eXpress manual.
Merge branch 'master' of https://github.com/chipster/chipster.git
Renamed slopBed, updated NGS tools list.