- kma - KeepMeAround: Intron retention detection in RNA-Seq
- fscca - Fast Sparse Canonical Correlation Analysis (written in Rcpp)
- Biclustering - ETA late February 2015
- Differential expression - ETA March 2015
I've made some contributions to the TopHat RNA-Seq aligner. In particular, I wrote the FASTA and transcriptome mapping modules (map2gtf), released since v1.4.0.
I also worked on a cloud-based mobile web application with Sergey Karayev and Adam Roberts called CabFriendly. You can find the code for it here and the poster for it here. Unfortunately the website is no longer being hosted.
There's some other random code of mine on GitHub, including config files.