Computational biology and genomics
This post contains the analysis steps used to create a differential gene expression results table generated from RNA-seq counts summarised using nf-core/rnaseq. The comparison was done between two conditions: normal versus (lung) cancer. We will be using {edgeR}, so install it if you haven’t already. if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("edgeR") We will also…
I have been using pnas_expression.txt as a test dataset for count table analyses for many years. It was created by Davis McCarthy and was hosted on their Google Sites website. After some time, the site became unavailable and I have been hosting it on my web server since then. The RNA-seq libraries were generated using…
It has been 14 years since I’ve started this blog and as per tradition, I write a blog post reflecting on stuff. It’s a loose tradition since some years I didn’t write anything. When I do write, it’s usually about something new I’ve learned and/or started practising since the last anniversary post. Recently, I’ve been…