Lukas Heumos

upheno.owl cannot be parsed with Pronto

4

``` Traceback (most recent call last): File "/home/zeth/PycharmProjects/bionty/ree.py", line 3, in test = Ontology("upheno.owl") File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/ontology.py", line 283, in __init__ cls(self).parse_from(_handle) # type: ignore File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/parsers/rdfxml.py", line 95, in parse_from...

Versionized download links

1

Hi, I'm having trouble finding versionized download links of upheno2. Do these exist somewhere? I don't always want to download the latest version (which is currently hosted where?!?) but ideally...

### Description of feature Title

### Description of feature `de_res_to_anndata` is not flexible enough: - [ ] Check whether it also works with less columns (no gene names, score, [....]). It must be more flexible...

Add dataloader for Jiang et al

1

### Description of feature https://www.biorxiv.org/content/10.1101/2024.01.29.576933v2.full https://zenodo.org/records/10520190

### Description of feature https://www.cell.com/cell-genomics/fulltext/S2666-979X(23)00339-7

Implement MCP methods

1

A reimplementation of https://github.com/livnatje/DIALOGUE could be awesome. Then we could also talk to @davidsebfischer et al. to see how far their MCP method is.

### Description of feature I think that our current structure is not SEO friendly

### Description of feature - [ ] Different names of parameters - [ ] Different parameters in general - [ ] Pass ax or create figure - [ ] save...

Consider merging a few multimodal datasets into Mudata objects

1

### Description of feature We currently have a few from scperturb that are single Anndata objects of modalities. Let's simplify this and create Mudata objects for these wherever possible/reasonable