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.

Genomes

genome.Genome(*, fasta, annotation[, ...])	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.
genome.GRCh37	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.
genome.GRCh38	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.
genome.GRCm38	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.
genome.GRCm39	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.
genome.hg19	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.
genome.hg38	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.
genome.mm10	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.
genome.mm39	A class that encapsulates information about a genome, including its FASTA sequence, its annotation, and chromosome sizes.

Motifs

datasets.cis_bp([unique])	A list of transcription factor motifs curated by the CIS-BP database.
datasets.Meuleman_2020()	A list of transcription factor motifs curated from [Meuleman20].

Raw data

datasets.pbmc500([type, downsample])	scATAC-seq dataset of 500 PBMCs from 10x Genomics.
datasets.pbmc5k([type])	scATAC-seq dataset of 5k PBMCs from 10x Genomics.
datasets.pbmc10k_multiome([modality, type])	Single-cell multiome dataset of 10k PBMCs from 10x Genomics.
datasets.colon()	scATAC-seq datasets of five colon transverse samples from [Zhang21].
datasets.cre_HEA()	Curated cis-regulatory elements from [Zhang21].