scVAE is a command-line tool for modelling single-cell transcript counts using variational auto-encoders.
Install scVAE using pip for Python 3.6 and 3.7:
$ python3 -m pip install scvae
scVAE can then be used to train a variational auto-encoder on a data set of single-cell transcript counts:
$ scvae train transcript_counts.tsv
And the resulting model can be evaluated on the same data set:
$ scvae evaluate transcript_counts.tsv
For more details, see the documentation, which include a user guide and a short tutorial.