Sep 22, 2014 — KEGG Human (hsa) Database for R — This morning I was trying to link some of my genes to pathways, so of course my first stop was KEGG. What in the world is KEGG? Kegg is a database of pathways. The pathway identifiers for human are numbered... Read more

Sep 18, 2014 — Basic awk to tweak data files! — Making an Annotation File for Genes I had the task to make a little annotation file (for use with vcftools) to annotate a big list of SNPs with genes, because I don’t speak “SNP” language. This turned into having fun... Read more

Sep 17, 2014 — Learning about VCF (variant call format) file analysis — If you just want to learn from the scripts I’m working on: SCRIPTS And as a subset of this post, if you want to learn about using awk to work with text files What is variant analysis? We all know... Read more

Aug 28, 2014 — Self Organizing Maps (SOM) — I have a thing for dimensionality reduction.  One method in particular, the Self organizing map, is probably my favorite.  I made this tutorial for my lab, but I thought it would be useful to share with the world of the... Read more