Musings on random things I've learned during my thesis work. Mostly computational biology with some genetics mixed for good measure.
RNA-seqeucning from xenograft experiments is increasingly being used in the context of precision medicine, drug screenings and cancer biology. However an often overlooked confounding factor is host-graft contamination. In this post, I address a few computational and wet lab approaches to managing this problem in RNA-seq data obtained from xenografts.
My favorites bar is filled up, so I'm dumping all my favorite bioinformatics-relevant tutorials below. General Bioinformatics Tutorials Biomedical Data Science (eBook) by Rafael Irizarry and Michael Love. This tutorial covers statistical modeling and inference, a little machine learning and has some great R based vignettes for RNAseq, ChIPseq and DNA CpG methylation analysis. Single […]
I found that installing the Circos package was a bit of a pain (especially in the newest version of OS X, El Capitan). So below I provide detailed, step-by-step setup instructions.