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By default, `SingleR` annotation uses references from the [`celldex` package](https://bioconductor.org/packages/release/data/experiment/html/celldex.html).
TODO: AVAILABLE REFERENCES ARE LISTED HERE.
Please consult the [`celldex` documentation](https://bioconductor.org/packages/release/data/experiment/vignettes/celldex/inst/doc/userguide.html) to determine which of these references, if any, is most suitable for your dataset.
`SingleR` reference files are formatted as `<singler_ref_name>_celldex_<celldex_version>_model.rds`.
For example, consider the reference file `BlueprintEncodeData_celldex_1-10-1_model.rds`:
- The reference name is `BlueprintEncodeData`.
- The `celldex` version is `1.10.1` (for the file name we substitute dashes for periods).
#### `CellAssign` references
By default, `CellAssign` annotation uses marker gene set references from [PanglaoDB](https://panglaodb.se/), as compiled by the Data Lab to represent common organ/tissue groupings.
TODO: AVAILABLE REFERENCES ARE LISTED HERE.
The specific organs used to compile marker gene references are listed in [`celltype-reference-metadata.tsv`](references/celltype-reference-metadata.tsv).
Currently #565 is establishing an approach to be able to quickly see all available models. We should update the instructions to point external users to those spots.
The text was updated successfully, but these errors were encountered:
After #502, we left some
TODO
s in theexternal-instructions.md
:scpca-nf/external-instructions.md
Lines 361 to 377 in 74b744b
Currently #565 is establishing an approach to be able to quickly see all available models. We should update the instructions to point external users to those spots.
The text was updated successfully, but these errors were encountered: