Index and biological spectrum of accessible DNA elements in the human genome

Data associated with the manuscript titled
"Index and biological spectrum of accessible DNA elements in the human genome"
https://doi.org/10.1101/822510

Code repositories for these data are available here:

• https://github.com/Altius/Index
• https://github.com/Altius/Vocabulary

Tab-separated file with DNase I Hypersensitive Site (DHS) coordinates,
including DHS summits and core regions and assignments to regulatory components.
A separate legend file describes the contents of each column in more detail.

• DHS_Index_and_Vocabulary_hg38_WM20190703.txt.gz
• DHS_Index_and_Vocabulary_hg19_WM20190703.txt.gz (mapped using liftOver, not ideal)
• DHS_Index_and_Vocabulary_legend.txt

Metadata files describing biosample characteristics and annotations,
provided in HTML, PDF, TSV and Excel formats:

• DHS_Index_and_Vocabulary_metadata.html
• DHS_Index_and_Vocabulary_metadata.pdf
• DHS_Index_and_Vocabulary_metadata.tsv
• DHS_Index_and_Vocabulary_metadata.xlsx

Presence/absence matrix of DHSs (rows) versus biosamples (columns),
provided in RData, MatrixMarket and raw formats:

• dat_bin_FDR01_hg38.RData
• dat_bin_FDR01_hg38.mtx.gz
• dat_bin_FDR01_hg38.txt.gz
• dat_bin_FDR01_hg19.RData (mapped using liftOver, not ideal)
• dat_bin_FDR01_hg19.txt.gz (mapped using liftOver, not ideal)

Normalized DNase-seq signal matrix of DHSs (rows) versus biosamples (columns),
provided in RData and raw formats:

• dat_FDR01_hg38.RData
• dat_FDR01_hg38.txt.gz

The order of DHSs (rows) is the same as in the DHS Index file(s) above,
and the order of biosamples (columns) is the same as in the metadata files.

Non-negative Matrix Factorization (NMF) results, decomposing the presence/absence matrix (hg38) into 16 components:

• 2018-06-08NC16_NNDSVD_Mixture.npy.gz
• 2018-06-08NC16_NNDSVD_Basis.npy.gz

Putative transcription factor-specific regulatory elements,
identified using DHS Vocabulary components, TF motif databases and biosample-specific footprinting data:

• TF_associated_DHSs_hg38.tar.gz