Make rlog transformation optional

[SusiJo]

Hi there,

when > 50 samples are used for differential gene expression analysis, the rlog transformation becomes very time consuming.
Currently, the transformed table is only used for saving and one quality control plot.
Therefore my suggestion would be to add an optional parameter --rlog [bool] that defines whether the transformation should be made or not. This would save much time when performing the analysis for a large number of samples.

[SusiJo]

Concerning the rlog in general, the RNAseq_Report.md needs to be updated because actually it's not the rlog transformation that is used for the PCA plots, but the vst transformation (see these lines: report-305, report-309, DESeq2.R-459 and DESeq2.R-472

[WackerO]

Closing this as it was addressed in #107 and #110