scrnaseq
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Multi-omics support (meta-issue)
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 multi
- [ ]
- TCR-seq (=RNA+TCR)
- TRUST4 (https://github.com/nf-core/scrnaseq/issues/71)
-
cellranger vdj
-
cellranger multi
- ATAC-seq (https://github.com/nf-core/scrnaseq/issues/174)
- [ ]
cellranger atac
(for only scATAC) - [x]
cellranger-arc
(RNA + ATAC) -> merged in #217
- [ ]
- 10x FFPE protocol (not strictly multimodal, but requires cellranger multi) (https://github.com/nf-core/scrnaseq/issues/247)
-
cellranger multi
-
Seems like support for cellranger multi will get us pretty far!
Once the alignment routes are implemented, we should also make the output of the workflow more user-friendly:
- https://github.com/nf-core/scrnaseq/issues/292
CC @heylf @fmalmeida
Hi @grst , Started running the tool with public data to get the gist of the tool and figure out how to work with the "input csv" for proper implementation.
Using this issue for backup of TODO existing in the implementation of multi-omics analyses.
Here, for the FFPE
, related to PR #276
- [ ] Discussion here about the simplification of the samplesheet parsing for
cellrangermulti
to avoid two different parsings. - [ ] Currently, BEAM data is not supported as part of #276