Seurat update #5339
Seurat update #5339
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remove one empty line
astrovsky01
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tools/seurat/macros.xml
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| </requirements> | ||
| </xml> | ||
| <xml name="norm" label="Normalizing data" expanded="true"> | ||
| <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" /> |
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min/max for integers and floats?
| <filter>@FUNCTION_CITE@</filter> | ||
| <filter>function['markers_file']</filter> | ||
| </data> | ||
| <data name="markers_cite_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} cite-seq on ${on_string}: Markers list"> |
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all tabular files should have a metadata section here to add the column names
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The current version is rigid and less practical. We probably have to make it modular like the Scanpy toolkit or even a similar set of tools as Scanpy. Then adding CITE-Seq or other modalities will be easier I guess. If you need CITE-Seq urgently, we can continue with the current structure in this update. |
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It has been requested that we add it asap. I don't mind future updates relatively quickly, but if we could get this feature in sooner, that would be appreciated. The rigidity of seurat is because seurat objects haven't historically been useable across other tools, so I made it a closed system. If that should be changed, I'm open to that being the step after this. |
add CITE-Seq test
fix linting and tests
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
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Thanks @nsoranzo! |
FOR CONTRIBUTOR:
Adds cite-seq functionality to seurat, permits intermediate output files, and early stops for partial runs