R

I just came back from the software-carpentry workshop held on April 2 and 3 at the University of Miami. The workshop link is here \ and the Etherpad:

I came across csvkit long time ago, but I just began to use it and found it is very handy. It is a python utility to manipulate csv files at command line.…

The question is very straightforward:\ I have three microarray or RNA-seq data sets (control, treatment1, treatment2, each should have several replicates…

dply is a nice R package to manipulate big data. There are several good tutorials I came across:

I had a post using mygene to convert gene ids. Bioconductor can do the same job.\ I put a gist on github.

we are on day 5 of the MSU NGS course. This morning, Ian Dworkin introduced some basic R.\ I found it refreshing and put a gist below.\ Pick one language…

My next-door PI wanted to look at the TRIM29 expression levels in a series of tumor xenografts from a microarray data. I used GEOquery bioconductor package…

I will defend next Tuesday. To relieve my anxiety a little bit, I decide to blog a little bit.

I will lay down the R code below

I’ve been collecting potential packages for (interactive) visualization of Genomic data.\ Here are the ones so far I’ve collected: