USeq Source Code

2. VCFAnnotator: New annovar versions can be incorporated more easily.
3. MethylationArrayScanner: New option for T-Test
4. SamAlignment: the 'chr' is no longer added to chromosomes. This would cause STP to create two versions of the chromosomes in the header.
5. SamTranscriptomeParser: Relaxed @SQ line matching
6. DefinedRegionDifferentialSeq: Fixed SAMSeq error when there was more than two conditions. New option to turn off DESeq2 independent filtering