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