lfcMLE may bring problems with low-expressed genes.

Also:
- Boxplots with labels turned 90 degrees
- do_deseq2 returns size factors

Library standedness was not taken into account correctly, and too many
reads in repeated regions were discarded in featureCounts:
<https://bioinformatics.stackexchange.com/q/2101/292>

Also added mean across replicates for bigwig files and use various log
fold change thresholds to classify genes.