TopHat aligner
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.

R packages
I'm currently working on two unrelated packages for RNA-Seq:

I anticipate on releasing them in the next few months.

CabFriendly
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.

Random stuff
There's some random code of mine on GitHub, including some outdated config files.