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Syncing #370 to main #371

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Nov 15, 2024
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Syncing #370 to main #371

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3782d76
Replace demux_sample_cell_estimate with demux_cell_count_estimate
jaclyn-taroni Nov 15, 2024
462e14d
Merge pull request #370 from AlexsLemonade/jaclyn-taroni/367-368
jaclyn-taroni Nov 15, 2024
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6 changes: 3 additions & 3 deletions docs/CHANGELOG.md
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Expand Up @@ -14,17 +14,17 @@ For more information about `AlexsLemonade/scpca-nf` versions, please see [the re

## 2024.11.14

* Recent versions of the raw count matrices in `SingleCellExperiment` and `AnnData` objects were not rounded.
* Recent versions of the raw count matrices in `SingleCellExperiment` and `AnnData` objects were not rounded.
The raw counts are now rounded to integer values in agreement with the documentation.
* Some project-specific metadata columns were renamed for uniformity:
* Columns previously labeled as `mycn_status` or similar with a gene name prefix are capitalized `MYCN_status`.
* Columns that were previously labeled with sentence case are now all lower case.
* Columns that were previously labeled with sentence case are now all lower case.

## 2024.10.14

* Some cell count-related fields in downloadable metadata have changed.
* `sample_cell_count_estimate` has been removed from downloads for non-multiplexed samples.
* A new field that indicates the estimated number of cells from a sample for a given library—`demux_sample_cell_estimate`—has been added to downloadable metadata for multiplexed samples.
* A new field that indicates the estimated number of cells from a sample for a given library—`demux_cell_count_estimate`—has been added to downloadable metadata for multiplexed samples.
This replaces the `sample_cell_estimate` field, which has been removed.
* Fusion nomenclature has been standardized using the double colon recommendation from the HUGO Gene Nomenclature Committee ([Bruford et al. 2021](https://doi.org/10.1038/s41375-021-01436-6)) in downloadable metadata.

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2 changes: 1 addition & 1 deletion docs/download_files.md
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Expand Up @@ -182,7 +182,7 @@ 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, the `demux_sample_cell_estimate` column will contain an estimate of the number of cells from the sample in the library (after demultiplexing) in the sample/library pair.
In addition, the `demux_cell_count_estimate` column will contain an estimate of the number of cells from the sample in the library (after demultiplexing) in the sample/library pair.


## Merged object downloads
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