Enable setting the count prior for empty droplets

broadinstitute / CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

https://cellbender.rtfd.io

BSD 3-Clause "New" or "Revised" License

297 stars 54 forks source link

Enable setting the count prior for empty droplets #233

Closed niklasmueboe closed 1 year ago

niklasmueboe commented 1 year ago

This PR would allow to let the user set the prior on the RNA counts of empty droplets in the CLI. This is useful if the estimation using the mode of the log(counts) does not give a reasonable estimate.

sjfleming commented 1 year ago

Thanks so much for contributing this @niklasmueboe !

Actually though, I've been working to do (what I think is) the exact same thing myself. That version is now included in v0.3.0

The new input arguments are called --force-cell-umi-prior and --force-empty-umi-prior.

So for now, I will mark this as closed by #238

sjfleming commented 1 year ago

But please let me know if the fix in v0.3.0 doesn't work for you, and we can look into re-opening this PR