chr/nochr option to htseq-count.R
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
Changes to DESeq
Added vm announcement installation
Add fruitfly to gb.
Merge branch 'master' of https://github.com/chipster/chipster.git
Add fruitfly to vm.
Removed edgeR classic trended dispersion, modified manuals
Merge branch 'master' of https://github.com/chipster/chipster.git
Reorganized ref genome list in Bowtie2, removed replicate parameter in
DESeq.
HTSeq modified so that it prints coordinates
Updates to PRINSEQ tools
edgeR classic bug fix
user-friendly exit added to ngs-create-experiment
Merge branch 'htseq-chr'
Two groups tests modified to handle zero variance elements
Replaced samtools -q 1 with Bowtie --no-unal to remove unaligned reads
from BAM