Differetial gene expression analysis options

[dbau]

Hi,

I am trying to find out the options used in biojupies to compute the Differential Gene Expression table. The paper states that:

The library consists of a set of core scripts responsible for loading the RNA-seq data into the pandas DataFrames (McKinney, 2010), scripts for normalizing the data, and scripts for performing the differential gene expression analysis, currently implemented with limma (Ritchie et al., 2015; Smyth, 2005) or the Characteristic Direction (Clark et al., 2014) methods.

However, I was not able to find in the documentation what limma and/or Characteristic Direction options are applied in the analysis. Could you please provide such an information and allow to manually set them?

Thanks a lot. Davide