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Add note about column names for multiplexed
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jashapiro committed Sep 23, 2024
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Expand Up @@ -183,6 +183,7 @@ Because we do not perform demultiplexing to separate cells from multiplexed libr
For more on the specific contents of multiplexed library `SingleCellExperiment` objects, see the {ref}`Additional SingleCellExperiment components for multiplexed libraries <sce_file_contents:additional singlecellexperiment components for multiplexed libraries>` section.

The [metadata file](#metadata) for multiplexed libraries (`single_cell_metadata.tsv`) will have the same format as for individual samples, but each row will represent a particular sample/library pair, meaning that there may be multiple rows for each `scpca_library_id`, one for each `scpca_sample_id` within that library.
In addition, an estimate of the total number of cells for each sample after demultiplexing will be found in the `sample_cell_estimate` (as opposed to the `sample_cell_count_estimate` column used for non-multiplexed samples).


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