This is a straightforward "normalization" method for scRNA-Seq and similar data, based on Sanity

Breda, Jérémie, Mihaela Zavolan, and Erik van Nimwegen. "Bayesian inference of gene expression states from single-cell RNA-seq data." Nature Biotechnology 39.8 (2021): 1008-1016.

Vanity implements this model in jax using standard mean-field variational inference to dramatically speed up inference, particularly when running on a GPU, and it works nicely with the anndata/scanpy ecosystem. Overall the goal is a faster more convenient Sanity for my own use, and hopefully of some interest to others.

Vanity seems to largely agree with with Sanity, with a slight tendency to produce lower values. This hasn't been exhaustively tested yet, so proceed with some caution.

Basic usage:

from vanity import normalize_vanity

normalize_vanity(adata) # where adata is an anndata.AnnData object