# Enhancer clusters for 833 epigenomes x 2M enhancers (Figure 3)
# Manifest:
cls_merge2_wH3K27ac100_300_assignments.bed
cls_merge2_wH3K27ac100_300_assignments.loc.bed
cls_merge2_wH3K27ac100_300_centers.tsv.gz
cls_merge2_wH3K27ac100_300_counts.tsv
cls_merge2_wH3K27ac100_300_rownames.tsv
cls_merge2_wH3K27ac100_300_nbp.tsv
modules_GO_enrichments_matrix_ordered.tsv.gz
collated_motifs.txt
logos/
motifs_bkgdhs_cls.enrich.full.tsv.gz
motifs_bkgdhs_cls_enrich.reduced.tsv.gz
motifs_bkgdhs_cls_enrich.full.fullnames.tsv
motifs_bkgdhs_cls_enrich.reduced.fullnames.tsv

# File descriptions:
## Cluster metadata:
cls_merge2_wH3K27ac100_300_assignments.loc.bed
- Cluster assignments.
- hg19 location (columns 1-3)
- Clusters (column 4) are 0-indexed (0:299).

cls_merge2_wH3K27ac100_300_centers.tsv.gz
- Centers matrix for clusters 

cls_merge2_wH3K27ac100_300_counts.tsv
- Number of enhancers per cluster.

cls_merge2_wH3K27ac100_300_rownames.tsv
- Epigenomic sample order for centers matrix.

cls_merge2_wH3K27ac100_300_nbp.tsv
- Number of base pairs covered per cluster.

## GO/Motif Enrichments:
modules_GO_enrichments_matrix_ordered.tsv.gz
- Matrix of 1892 GO enrichments (using GREAT) across 300 modules.

collated_motifs.txt
- PFMs for 1689 motifs used in motif enrichment analyses (JASPAR core 2018, HOCOMOCOv11, and Jolma 2013 HT-SELEX)

logos/
- Motif logos for the 1689 motifs above.

motifs_bkgdhs_cls.enrich.full.tsv.gz
- Motif enrichment matrix for all motifs with any level of enrichment (1682 motifs) against 300 modules (c0:c299)

motifs_bkgdhs_cls_enrich.reduced.tsv.gz
- Motif enrichment matrix for archetype motifs with absolute log2FC>=1 (160 motifs) against 300 modules (c0:c299)

motifs_bkgdhs_cls_enrich.full.fullnames.tsv
- Full motif names mapped to the shortened motif names in the full matrix.

motifs_bkgdhs_cls_enrich.reduced.fullnames.tsv
- Full motif names mapped to the shortened motif names in the archetypes matrix.