Johannes Ostner

Hi @karenlawwc! I'm not 100% sure what the term "reference" in your question refers to. Do you mean the categories in your composition (cell types) or the levels of a...

Yes, I'd do a pairwise comparison of all three levels. Changes in compositional data are not symmetric (say, an increase by x units from condition 1 to condition 2 corresponds...

Hi @wdg118! Each pairwise comparison works just as a normal scCODA model (Final parameter != 0 --> credible effect). For comparing runs of scCODA on different pairs of conditions, you...

Exactly! You can set the FDR to a desired level and the model will select the credible effects based on their bayesian inclusion probability, controlling for multiple comparisons. You can...

Hi! Yes, scCODA supports the use of multiple variables from different types. You have to make sure that your numeric variables are normalized, though. Otherwise, their effects might become very...

Hi @alefrol638, Thanks for your request! We're currently in the process of reimplementing scCODA with new plotting and data integration methods, and will actually implement a plotting option for this...

Thanks for spotting this! I'll keep this fix in mind if we ever release a new version of this package. The actively maintained implementation of scCODA in the [pertpy](https://github.com/theislab/pertpy) package...

I'll leave it open for now, so that I won't forget about this fix. Thanks again!

Hi @Marwansha! What range is your covariate in? You should make sure that your continuous covariates are normalized before applying scCODA

Hmmm, that's strange. Are you using only the continuous covariate, or are you including it in a formula together with other covariates? Could you also maybe share the extended summary...