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Changelog for updates to consensus #487

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allyhawkins merged 2 commits into from
Feb 4, 2026
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Changelog for updates to consensus #487

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add changelog about consensus updates
allyhawkins Feb 3, 2026
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Expand Up @@ -12,6 +12,16 @@ For more information about `AlexsLemonade/scpca-nf` versions, please see [the re
<!-- PUT THE NEW CHANGELOG ENTRY RIGHT BELOW THIS -->
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## TODO: ADD DATE

* Consensus cell types have been updated to fix a minor bug in assigning labels.
Previously, if two out of three methods (`SingleR`, `CellAssign`, and `SCimilarity`) agreed but the third method was unable to classify a cell, the consensus cell type was incorrectly classified as `Unknown`.
The consensus cell types have been updated so that if two out of three methods agree the consensus cell type is assigned with the appropriate label using an ontology-based approach, regardless of whether or not the third method is able to classify the cell.
* See the {ref}`documentation on cell type annotation<processing_information:cell type annotation>` for more information on how consensus cell type are assigned.
* See the {ref}`the single-cell gene expression file contents page<sce_file_contents:singlecellexperiment cell metrics>` page for more information on where to find cell type annotations in the processed objects.
* The `infercnv_success` status previously reported in the metadata of `SingleCellExperiment` objects and `uns` of `AnnData` objects has been renamed as `infercnv_status` .
For more information, see {ref}`the single-cell gene expression file contents page<sce_file_contents:singlecellexperiment cell metrics>`.

## 2026.01.08

* Data on the Portal can now be downloaded in three different ways:
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