Installing DESeq2 with a conda R setup

We've had some users report difficulties installing the DESeq2 R library on Windows so i've put together this small repo containing some instructions of how i've successfully managed to get this working.

This setup requires Anaconda and installs DESeq2 version 1.26.0 and along with R 3.6.1 and RStudio plus associated dependencies.

Workflow

To get started we need to create a new environment using the .yml file included in this repo. In the Anaconda Navigator:

# either navigate the the directory containing the .yml file in this repo and run:
conda env create -f environment.yml

# or create without the yml file with the line
conda create --name deseq2-env -c conda-forge r-base=3.6.1 rstudio r-foreign

This will install R 3.6.1, RStudio and the R package foreign and dependencies which should allow for the installation of DESeq2.

Next open R either via RStudio or via the R IDE and use the following commands summarised in the install_deseq2.R file:

install.packages("BiocManager")

BiocManager::install("DESeq2")
# you may be prompted to update some installed packages. We recommend selecting S (for some).

# test the install has succeeded 
library(DESeq2)