Introduction

This site provides the documentation on the BABS bulk RNASeq pipeline. There are several somewhat distinct aspects to the documentation, and they’ll be covered on this site:

• The nature of the ‘spec’ file that determines the statistical analysis that will be carried out on the data. This is the most important document in your understanding of the benefits the pipeline can bring.

• What to do once you’ve got such a starting point for a new project. Users of the template will want to start here.

• How the github repository turns itself into the starting point for a new project (e.g. obviously we don’t want all the meta information, like this page, ending up in a user’s project). I’m currently bringing over the functionality we use for stats projects which is much cleaner than the current approach, so this isn’t yet documented.

• How to add extra functionality to the RNASeq template. People wanting to develop extra template functionality will want to start here.

• How to apply the methodology to an existing DESeqDataSet or SummarizedExperiment object (or even a CSV file of data), so that we can use the functionality of a spec file with preprocessed data more easily. This documentation is work-in-progress.