Marcel Schilling

Missing `rpy2` (optional) dependency?

6

### Please make sure these conditions are met - [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on...

add (optional) `rpy2` dependency for `milo`

3

**PR Checklist** - [x] Referenced issue is linked - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] Documentation in...

MA plots for DE results

1

### Description of feature I noticed that all DE examples use Volcano plots to summarise/visualize the results. I prefer MA plots as I consider Volcano plots to over-emphasize the importance...

I wrote the following RMarkdown document to illustrate my issue and proposed solution (just copy it to a file and render it to an output format of your choice): ````rmarkdown...

fix(nginx): Handle large header responses for root

4

### ☑️ Resolves * See https://help.nextcloud.com/t/resolved-502-on-nextcloud-root-after-update/233954/11. ### 🖼️ Screenshots I do not know how to locally build and render the documentation but I only added a few lines to the...

mismatch of documentation and implementation regarding how to specify design for DESeq2.

1

The docstring claims `design` should be a `formula` when `method="DESeq2"`: https://github.com/HelenaLC/muscat/blob/49a3b323133921fdcd9772441df0aa2ee09ab1e1/R/pbDS.R#L13 However, `pbDS` calls `.check_args_pbDS` before considering `method`: https://github.com/HelenaLC/muscat/blob/49a3b323133921fdcd9772441df0aa2ee09ab1e1/R/pbDS.R#L95 That function immediately fails if `design` is anything but a `matrix`:...