Showing posts from March, 2023

A docker image for infinum methylation analysis

Performing a differential methylation analysis of infinium array data requires an impressively large number of R packages, such as `minfi`, `missmethyl`, `limma`, `genomicRanges`, `DMRcate`, `bunpHunter` and many others. Each of these in turn are considered heavy packages as they each require many dependancies. This means it can take up to an hour to go from a vanilla R installation to one with all the needed packages installed. If you are using multiple computers you might find that these have slightly different versions of R, bioconductor and this large stack of dependancies, which could lead to different results. You may also find that it is difficult to install this large set of dependancies on shared systems, as some dependenncies might require installation of system libraries that need admin permissions to install. The way I've tried to alleviate this problem is to install all my needed packages into a Docker image which can then be downloaded and run in a few minutes on a ne