Dylan Cable
Dylan Cable
Thank you all for pointing out this issue and solution. If the issue is with the `doParallel` / `foreach` packages, then I'm not sure there is anything we can do...
Yes, see `import_weights` . When you run C-SIDE, you need to use full mode rather than doublet mode in this case.
Can you test with 1 core or with a subset of your dataset? Other ideas for debugging: in the `runRCTD.R` code, there are commented out lines for either print statements...
Apologies -- I don't have experience working with the python version of RCTD. I would encourage you to contact the developers. If you are having trouble getting a response, you...
RCTD works best when the reference is most similar as possible to the ST. Cross-species would be pushing those limits. In practice, you can try the reference and see how...
`UMI_min` filters cells. `counts_MIN` filters genes.
Hi Eli, Thank you for your question. RCTD works on raw counts. RCTD has it's own normalization method. You are allowed to filter cells or genes using your preferred approach....
Good question! It is possible to get such scores out of RCTD, but it is not necessarily something that is stored by RCTD by default. The relevant score would be...
Yes, there is actually a mode of RCTD that would accomplish this task well. Please see the `fitBulk` function within RCTD. This is used in the platform effect normalization step...
1. For visualization issues, we don't recommend using the RCTD plots for these kinds of intense cases. You can adapt the RCTD plots to make your own ggplots. My playing...