HDMA Global BPCells Files

This is the BPCells fragment files, count matrices and object for HDMA (Liu*, Jessa*, Kim*, Ng* et al, bioRxiv 2025). Note that BPCells package uses on-disk storage, so the fragment files and count matrices in the RDS object only point to the path where the files are stored, and it's important to modify those paths when the folders are moved.

The BPCells RDS object contains:

cell_metadata: the per cell metadata

frags: path to unzipped folder of ATAC fragments 'ATAC_merged'

rna: path to unzipped folder of unnormalized decontX'ed RNA count matrices 'RNA_merged'

rna_raw: path to unzipped folder of unnormalized raw RNA count matrices 'RNA_raw_merged'

transcripts: GENCODE human release 42 gene annotation

loops_p2g: Peak2Gene loops per organ or globally across organs

loops_abc: ABC loops per L1 cluster

peaks: HDMA global acCREs

hits: all ChromBPNet motif instances