diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index 2bb3418..5a538f8 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -12,6 +12,16 @@ For more information about `AlexsLemonade/scpca-nf` versions, please see [the re +## 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` for more information on how consensus cell type are assigned. + * See the {ref}`the single-cell gene expression file contents page` 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` and now contains a string instead of boolean value. +For more information on the contents of this value, see {ref}`the single-cell gene expression file contents page`. + ## 2026.01.08 * Data on the Portal can now be downloaded in three different ways: