My research is about developing statistical models to solve genomic problems.
More specifically, I am working on highly repetitive regions of the genomes, building models to assign multi-mapping reads to its potential alignment positions. We proposed Perm-seq which aligns multi-mapping ChIP-seq reads. The R package permseq is available on github.
Currently, we are working on the three-dimensional organization in repetitive regions of the genomes.
I highly recommend Emacs especially for researchers working frequently on UW-Madison stat/biostat server.
ENCODE, short for Encyclopedia of DNA Elements. Users can batch download extraordinary large amount of data sets in human genome with functional annotations.
HiCPlotter: Fancy! User friendly tool for Hi-C result visualization.
WashU Epigenome Browser: Even Fancier! Powerful genome browser which I also use for Hi-C result visualization.
A very clean and relatively comprehensive bash cheat sheet
If you are interested in STAN with application to Bayesian Inference, blogs @ baconzhou's blog are recommended.