scvi.data.dataset_10x

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scvi.data.dataset_10x#

scvi.data.dataset_10x(dataset_name=None, filename=None, save_path='data/10X', url=None, return_filtered=True, remove_extracted_data=False, **scanpy_read_10x_kwargs)[source]#

Loads a file from 10x website.

Parameters:

  • dataset_name (str | None (default: None)) – Name of the dataset file. Has to be one of: “frozen_pbmc_donor_a”, “frozen_pbmc_donor_b”, “frozen_pbmc_donor_c”, “fresh_68k_pbmc_donor_a”, “cd14_monocytes”, “b_cells”, “cd34”, “cd56_nk”, “cd4_t_helper”, “regulatory_t”, “naive_t”, “memory_t”, “cytotoxic_t”, “naive_cytotoxic”, “pbmc8k”, “pbmc4k”, “t_3k”, “t_4k”, “neuron_9k”, “pbmc_1k_protein_v3”, “pbmc_10k_protein_v3”, “malt_10k_protein_v3”, “pbmc_1k_v2”, “pbmc_1k_v3”, “pbmc_10k_v3”, “hgmm_1k_v2”, “hgmm_1k_v3”, “hgmm_5k_v3”, “hgmm_10k_v3”, “neuron_1k_v2”, “neuron_1k_v3”, “neuron_10k_v3”, “heart_1k_v2”, “heart_1k_v3”, “heart_10k_v3”, 5k_pbmc_protein_v3”, “5k_pbmc_protein_v3_nextgem”, 1M_neurons”.

  • filename (str | None (default: None)) – manual override of the filename to write to.

  • save_path (str (default: 'data/10X')) – Location to use when saving/loading the data.

  • url (str (default: None)) – manual override of the download remote location. Note that we already provide urls for most 10X datasets, which are automatically formed only using the dataset_name.

  • return_filtered (bool (default: True)) – Either filtered data or raw data.

  • remove_extracted_data (bool (default: False)) – Whether to remove extracted archives in the case of .tar.gz downloads.

  • **scanpy_read_10x_kwargs – Kwargs for scanpy’s read_10x function

Return type:

AnnData

Returns:

adata initialized with 10x data

Examples

>>> import scvi
>>> neuron = scvi.data.dataset10X("neuron_9k")
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