Enhancements

[itsvenu]

• multiBigwig_summary - include peaks_df argument. Which can compute enrichments at peaks provided externally (this ignore the bed_path from sample table)

• plot_saturation_curve

• get_motif_enrichments - perform de novo/known motif enrichments for a given set of peaks. Further filter by peak strength of motif enrichment signal to output good quality results

• correlate_enhancer_gene - epigenomics signal vs gene expression to associate open-chromatin regions with genes

• Integrate diffBind? Requires BAM file paths in sample_table. But all downstream processes will be very easy in ALPS once diffBind spits out the results.

• enrichTF/TFBStools - for TF enrichment analysis

• enhancer associated regulatory networks: https://github.com/bhklab/CREAM & https://genome.cshlp.org/content/early/2019/09/18/gr.248658.119

• profile plots of regions - extract line plots from enrichedHeatmap. Options should be group level, sample level