Gregor Sturm

Extend PyDESeq2 class to support arbitrary contrasts and designs

1

### Description of feature Blocked by https://github.com/owkin/PyDESeq2/issues/213 See also https://github.com/theislab/pertpy/blob/2cc7ff77695cb616bb3ab207b5e506c0880aadb1/pertpy/tools/_differential_gene_expression/_pydeseq2.py#L62-L69 Migrated from https://github.com/scverse/multi-condition-comparisions/issues/13

Alternative way to get genomic positions

2

### Description of feature Currently the only way to get genomic positions is through reading a GTF file. This is (a) slow and (b) gtfparse repeatedly makes problems. It could...

### 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...

### 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...

Closes #549. - [ ] CHANGELOG.md updated - [ ] Tests added (For bug fixes or new features) - [ ] Tutorial updated (if necessary)

Dealing with alleles and multiple gene calls

4

I want to report some kind of bug/issue that I recognized during my work in Scirpy and has to do with scirpy.tl.define_clonotype cluster (but likely also with scirpy.tl.define_clonotype, although this...

it was temporarily pinned because 0.10.9 broke muon and dandelion

Follow up on https://github.com/scverse/scirpy/pull/512 * I think I would somewhat prefer that the histogram result is stored in AnnData and have a separate plotting function (to be consistent with the...