Datasets

Every tutorial on this site uses one of these. They are hosted on Zenodo and fetched on demand:

import piaso

piaso.data.list_datasets()                       # what is available
piaso.data.fetch_dataset("mouse_brain_10k_gemx") # download, returns a path
adata = piaso.data.load_dataset("mouse_brain_10k_gemx")   # download and open

Files are cached under ~/.piaso/data/datasets/ and verified against a checksum, so a download interrupted half way is re-fetched rather than silently used. Calling fetch_dataset again on a complete file is instant.

Name	Description	Species	Cells	Size
piaso_markerdb_allen_immune	PIASOmarkerDB Allen Human Immune Health Atlas L2	human	—	0 MB
e18_v3_nuclei	E18 Mouse Brain Nuclei 5K v3.1 (10x Genomics)	mouse	5,000	19 MB
e18_v3_cell	E18 Mouse Brain Neurons 10K v3 (10x Genomics)	mouse	10,000	45 MB
e18_v4_cell	E18 Mouse Neurons 10K GEM-X v4 (10x Genomics)	mouse	10,000	65 MB
mouse_brain_10k_gemx	10K Mouse Brain GEM-X v4 (10x Genomics)	mouse	11,357	66 MB
pbmc_multiome_san1	Human PBMC snMultiome SAN1 (De Rop 2024)	human	3,545	73 MB
pbmc_multiome_san2	Human PBMC snMultiome SAN2 (De Rop 2024)	human	4,360	84 MB
adult_cortex_multiome_rna_cytome	Adult mouse cortex multiome RNA (cytome)	mouse	—	192 MB
sea_ad_mtg_20k_cytome	SEA-AD middle temporal gyrus, 20k nuclei (cytome)	human	—	269 MB
humandevcx_38_rna	Human developing cortex snRNA, 38 samples (cytome)	human	—	1.1 GB
allen_devvis_rna	Allen developing mouse visual cortex snRNA, 200k nuclei (cytome)	mouse	—	1.4 GB
sea_ad_mtg_20k	SEA-AD MTG 20K subsample (raw)	human	20,000	1.8 GB
adult_cortex_multiome_rna	Adult Mouse Cortex Multiome RNA (P57)	mouse	17,412	2.5 GB
humanlifespan_pfc_rna	Human lifespan prefrontal cortex snRNA, 1.5M nuclei (cytome)	human	—	25.7 GB

Using your own data

Nothing here is required — every tutorial works on your own Cell Ranger output:

adata = piaso.pp.read_10x("path/to/filtered_feature_bc_matrix.h5")