The one missing data issue to rule them all

[Zethson]

• [ ] QC needs update
• [ ] Clustering
• [x] Annotation
• [ ] Data integration
• [x] DGE (should be solved already with @alitinet PR)
• [x] GSEA/Pathway can use the pertpty dataloader (but has the dataset generally)
• [ ] GRN
• [x] CCC (Why Kang 25k?) - it's just the normal Kang, right? Then use pertpy
• [ ] Bulk deconvolution
• [ ] ATAC intro
• [ ] ATAC QC
• [ ] ATAC GRN
• [x] CITE QC
• [x] CITE norm
• [x] CITE doublet
• [x] CITE dim red
• [x] CITE batch
• [x] CITE annotation
• [ ] AIRR clonotype
• [ ] TCR specificity (comes from AIRR immune receptor profiling)
• [ ] AIRR multimodal integration (comes from AIRR immune receptor profiling)
• [ ] Multimodal paired
• [ ] Multimodal advanced

[WeilerP]

@Zethson, the RNA velocity dataset is downloaded automatically via scVelo. Do you still want the data on the best practice's figshare?

[Zethson]

@WeilerP no absolutely not and I accidentally didn't scroll far enough. Sorry and thanks! it's all good.

[hai178912522]

Wow! You guys did a really great job. It's much easier to learn now! Thank you very much for your efforts.

[hai178912522]

Hello, I would like to ask how long it takes to complete the data upload

[AnnaChristina]

Hi @hai178912522, we are on it! As you can imagine there are more people involved (authors of the chapters, core best practices team, etc.) and I do not have access to all data parts myself, but depend on a few people to share the data upfront. Additionally, it is holiday season in europe, so please be a little bit more patient, we are on it. thanks!

[AnnaChristina]

cannot change the GSEA/Pathway data loading to pertpy as it changes results bc of dependency issues

[AnnaChristina]

CCC - Then use pertpy -> not working due to dependency issues