CiteSeqDataset

class scvi.dataset.CiteSeqDataset(name='cbmc', save_path='data/citeSeq/', delayed_populating=False)

Bases: scvi.dataset.dataset.DownloadableDataset

Allows to form 3 different CiteSeq datasets.

Note that their centered log ratio transformation for ADT counts is different from the standard clr transformation: they explain they add pseudocounts (for 0 values), but do not explicit the actual transformation. It doesn’t seem to be simply adding count 1 to all entries, or only 0 entries.

Parameters

• name (strstr) – Name of the CiteSeq dataset to load. Either “cbmc”, “pbmc” or “cd8”.

• save_path (strstr) – Location to use when saving/loading the data.

• delayed_populating (boolbool) – Switch for delayed populating mechanism.

Methods Summary

populate()

Populates a DonwloadableDataset object’s data attributes.

Methods Documentation

populate()

Populates a DonwloadableDataset object’s data attributes.

E.g by calling one of GeneExpressionDataset’s populate_from... methods.