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Update docs/CHANGELOG.md
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Co-authored-by: Joshua Shapiro <[email protected]>
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jaclyn-taroni and jashapiro authored Aug 12, 2024
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Expand Up @@ -18,7 +18,7 @@ For more information about `AlexsLemonade/scpca-nf` versions, please see [the re
* This column indicates if the age specified in the `age` column is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`.
* This will also be present in the metadata of the `SingleCellExperiment` and `AnnData` objects.

* AnnData objects have been updated to ensure compatibility with [`Scanpy`](https://scanpy.readthedocs.io/en/stable/).
* AnnData objects have been updated to improve compatibility with [`Scanpy`](https://scanpy.readthedocs.io/en/stable/).
* PCA and UMAP embeddings are now stored as `X_pca` and `X_umap` (previously `X_PCA` and `X_UMAP`).
* A new column has been added to the `.var` slot, `highly_variable`, indicating if the given gene can be found in the list of highly variable genes.
* Parameters and variance weights associated with the PCA results is now available in `.uns["pca"]`.
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