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

Data associated with the manuscript titled<br> "Index and biological spectrum of accessible DNA elements in the human genome"<br> https://doi.org/10.1101/822510 Code repositories for these data are available here: https://github.com/Altius/Index https://github.com/Altius/Vocabulary <br> Tab-separated file with DNase I Hypersensitive Site (DHS) coordinates,<br> including DHS summits and core regions and assignments to regulatory components.<br> 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,<br> 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),<br> 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),<br> 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,<br> 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,<br> identified using DHS Vocabulary components, TF motif databases and biosample-specific footprinting data: TF_associated_DHSs_hg38.tar.gz