Some cell profiles contain a large majority of reads mapping to a single gene (e.g. the Rn45s locus for low quality cells). These cells are usually filtered out during quality control, but in the event they persist in a dataset passed to scnym, they can lead to unstable training dynamics and failures to converge.
We should add simple quality control checks in .api.scnym_api that search for these cells in user provided datasets and throw a warning if they appear.
Some cell profiles contain a large majority of reads mapping to a single gene (e.g. the
Rn45slocus for low quality cells). These cells are usually filtered out during quality control, but in the event they persist in a dataset passed toscnym, they can lead to unstable training dynamics and failures to converge.We should add simple quality control checks in
.api.scnym_apithat search for these cells in user provided datasets and throw a warning if they appear.