Posts

Talk to a computational biologist scientist from the idea not the data

The mistakes and the success of building as fastest as possible the infrastructure

Finally tired of the broken TP holder and how to make a trip to Home Depot a 2 months project.

My personal experience with cancer and how much work still to do

My personal experience giving up on academia to bet on industry

I found myself to force to use cellranger. Meanwhile it helps a lot to run from bcl files to single cell counts matrixes, I discovered that is quite difficult to control many options related to optimization.

We use bcbio-nextgen for the analysis of sequencing data, mainly, (sc)RNAseq, smallRNAseq, DNASeq and ChIPSeq. It is not rare that we get collaborators who wants to re-analyze public data-set. Inside bcbio, we have bcbio_prepare_samples.

This post will show how to configure quickly the colors for the annotation of rows/columns that go on top or on the side of a heatmap. I normally use pheatmap a lot.

This post should show you an easy way to get the following data type integrated into a figure: functional enrichment analysis gene expression data from any technology miRNA expression data from any technology I am using the function isoNetwork from the package isomiRs, that of course is developed by me :) My ego is not that big, it is just I wanted a figure showing that information, and I couldn’t find any at a time, but if you know any, tweet me about it to @lopantano.

This is a funny story, and I will try to tell you how I realized I don’t know anything about R in 400 words. I work at the Bioinformatic Core at Harvard TH School.