SCT v2 models - Githubissues

satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

GNU General Public License v3.0

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SCT v2 models #109

Closed saketkc closed 2 years ago

saketkc commented 3 years ago

Support for fixing slope and intercept
Support for choosing between arithmetic and geometric mean in default and offset models
Add scale_factor option to define a custom scale factor covariate for correcting counts
Allow plotting residual variance vs gene mean plot with respect to arithmetic mean

ChristophH commented 3 years ago

Hi Saket, this looks great.

Could you write a short paragraph (one or two sentences with examples or motivation) in each change/addition to the package (when it is not self-explanatory)? This would go into the news section of the README and the NOTES file.

I'll try to have a look at all the detail in this PR fairly soon and then make it part of release 0.3.3 in mid July

cnk113 commented 3 years ago

Sorry to barge in, but I've been using the v2 model. With the latest changes is there a reason n_cells is fully overridden to 2000 cells? Having the default or otherwise set by the user as it was is fine?

saketkc commented 3 years ago

Thanks for pointing it out @cnk113, I will fix it.