Will Townes

Great package! I would be interested to see the Negative Binomial as an option (the user could provide a fixed value of the dispersion parameter "phi" to make it a...

have you had a chance to look at this?

I should note that kallisto does not throw any errors or warnings, and the output shows that it processed 13,004,694 reads but only 2,307,233 reads pseudoaligned

I am also interested in this! I would like to be able to do Wald tests with glmGamPoi. Currently I figured out a hack which others may find useful. Note...

@const-ae thanks! So first of all I am actually doing this on neuroscience data not genes but I noticed many times on my data the F-statistic from the `test_de` function...

Sorry I can't provide the example right now, it's not public data (yet) and my coauthors aren't comfortable with me sharing it until after the publication unfortunately. But I can...

I have the same issue.

Hi Jan, thanks for sharing these interesting results. Yes, it's very possible that the Poisson GLM-PCA is stopping too early. I'm glad you were able to use the deviance trace...

Hi, thanks for your interest in the package. It is similar to RUV/ SVA in that you are fitting both a factor model and a regression model. However, in GLM-PCA...

Apologies for the delay in responding. I unfortunately don't have the bandwidth to maintain this code base the way I would like. Am I correct to assume that your model...