Gregor Sturm
Gregor Sturm
### Description of feature The mtx conversion has grown organically over time and seems error-prone and overly complex. Also with the new emptydrops #301 cell calling, matrices need to be...
### Description of feature Universc is currently broken (it likely was for a while, because tests were running with the `-stub` option). Prerequisite to make it work would be to...
### Description of feature cellrangerarc is currently not tested as part of the CI workflows. Once #91 is set-up, we should add a testcase for cellranger-arc. Some testdata should be...
### Description of feature When processing multimodal data (e.g. CITEseq via cellranger multi, RNA+ATAC via cellranger-arc), we should not only generate a single AnnData/h5ad object, but instead combine the modalities...
### Description of feature This issue is to provide an overview of different tools and related sub-issues related to supporting multiple modalities: - CITE-seq (=RNA+protein) (https://github.com/nf-core/scrnaseq/issues/99) - [ ] `cellranger...
### Description of feature https://www.biorxiv.org/content/10.1101/2023.03.17.533215v1.article-info It provides a standardized format definition for sequencing libraries and works together with Alevin-fry, kb and starsolo as shown in their example: 
### Description of feature Folow up of #160 by @kafkasl. We don't yet add gene symbols in the output files when using alevin-fry as aligner. > As per [this discussion...
I have a case where a certain gene appears twice in the results table. This is annoying, because in that case I can't merge it back into an AnnData object....
Hi @JJAlmagro, please consider adding a LICENSE file to your repository. Without it, nobody is legally allowed to run the scripts from this repository. In particular, I would be interested...
Hi, could you please publish the versions of the python packages you're using (e.g. using `pip freeze`)? I fail to run the minimal example `python train.py -i train.npz -t test.npz`...