Lukas Heumos

Remove all Binder buttons

5

^ CC @VladimirShitov

Data infrastructure

7

Answers questions like 1. How to get data 2. Where to get data from 3. Sfaira 4. ....

The one missing data issue to rule them all

8

- [ ] QC needs update - [ ] Clustering - [x] [Annotation](https://figshare.com/articles/dataset/Luecken_multiome_human_bone_marrow_2021_s4d8_cellular_structure/23586042) - [ ] Data integration - [x] DGE (should be solved already with @alitinet PR) - [x]...

TCR/BCR enhancements

6

- [ ] Review by BS - [x] Tessa etc output in multimodal integration way way too verbose. Silence it - [ ] Update https://www.sc-best-practices.org/air_repertoire/ir_profiling.html#immune-receptor-sequencing for latest manuscript changes ->...

Title

Create massive container with separate Conda environments

1

`find . -name "*_environment.yaml" | xargs mamba env create -f` Would have to try out whether it becomes too big or not

Discuss various MCP approaches and maybe demonstrate DIALOGUE & expimap or so?

citations broken for bulk deconvolution

2

e.g. https://www.sc-best-practices.org/deconvolution/bulk_deconvolution.html#approaches Cannot reproduce locally. Already redeployed. IDK what's happening.

Host the datasets somewhere else

2

Figshare is terrible. Let's see whether we can switch to Huggingface