Datasets

These functions facilitate the download of public datasets and auxiliary data used in the SnapATAC2 package.

Note

You can change the data cache directory by setting the SNAP_DATA_DIR environmental variable.

Genome

genome.Genome(chrom_sizes, annotation_filename)
genome.GRCh37
genome.GRCh38
genome.GRCm38
genome.GRCm39
genome.hg19
genome.hg38
genome.mm10
genome.mm39

Motifs

datasets.cis_bp([unique])	Motifs from CIS-BP database.
datasets.Meuleman_2020()	Motifs from CIS-BP database.

Raw data

datasets.pbmc500([downsampled])	500 PBMCs from 10x Genomics.
datasets.pbmc5k([type])	5k PBMCs from 10x Genomics.
datasets.pbmc10k_multiome([modality, type])	10k PBMCs from 10x Genomics.
datasets.colon()	5 colon transverse samples from Zhang et al., 2021.
datasets.cre_HEA()	cis-regulatory elements from Zhang et al., 2021.