In each folder, the sh files describe the sequence of analyses that were performed.
- R32 - corresponds to R installation with Bioconductor version 3.2
- R31 - Bioconductor version 3.1
- R214 - Bioconductor version 2.14
R packages:
- DRIMSeq version 0.3.3
- dirmult version 0.1.3-4
- sQTLseekeR version 2.1 (downloaded on October 14th, 2015)
- DEXSeq version 1.10.8 (Bioconductor release 2.14)
Other:
- SRA toolkit - fastq-dump
- TopHat version 2.0.14
- Bowtie2 version 2.1.0.
- kallisto version 0.42.1