ChIP-seq: differential peak calling and more

[tovahmarkowitz]

New features:

• Differential peak calling - set up to use DiffBind if there are replicates and MaNorm when there are no replicates
• Uropa: annotation tool, runs 4 ways: all genes and no bias toward position relative to genes, all genes with a TSS focus, only protein coding genes with no bias, and only protein coding genes
• DiffBind and Manorm outputs will be annotated by Uropa
• Heatmaps in QC half will now create a plot at only protein coding genes along with the previous plots
• Additional multiQC step added to the QC pipeline half that will be created independent of ppqt outputs
• Jaccard plots are created and placed in PeakQC
• Also adjusting the effective genome size to be the same across tools (mostly affects mouse analyses)
• And a few other minor details.