As of November 2023, the CHANGELOG is a feature of our documentation we’ll use to report and summarize changes to downloads from the ScPCA Portal.

You can find more information about how and when your download was prepared in the following places:

  • The date your download was packaged (Generated on: {date}) is included at the top of the README in your download.

  • The version of the AlexsLemonade/scpca-nf pipeline used to process data in your download is included in the workflow_version column of the single_cell_metadata.tsv or bulk_metadata.tsv file in your download. For more information about AlexsLemonade/scpca-nf versions, please see the releases page on GitHub.


  • AnnData objects are stored in files that now have the extension .h5ad instead of .hdf5.

  • A preprint describing the ScPCA Portal and the pipeline used to process data is now available on bioRxiv (DOI: 10.1101/2024.04.19.590243). Please cite this preprint when citing the ScPCA Portal (see How to Cite for more information).


  • When downloading data for an entire project, you have the option to download a single file with a single merged object containing all gene expression and metadata for all samples in that project.

    • These merged objects are available as either SingleCellExperiment (.rds files) or AnnData (.hdf5 files) objects.

    • This option is available for most projects. If the project you are interested in does not have this option, see our FAQ on which projects can be downloaded as merged objects.

  • Merged project downloads will contain a brief summary report about the merged object as well as the individual QC and cell type annotation reports for all libraries in the merged object.

  • See our documentation on how merged objects were created and our FAQ about merged objects for more information.


  • Cell type annotations are now included in each download. Cells were annotated using both SingleR and CellAssign.

  • Downloads also contain a separate cell type report providing more information about cell type annotations, including comparisons between different cell type annotations and diagnostic assessments of cell type annotation reliability.

  • Sample metadata now includes two additional pieces of information which can be used to filter datasets: Whether the given sample is a patient-derived xenograft, and whether the sample is derived from a cell line.

  • Processed SingleCellExperiment objects no longer include the full miQC result object in their metadata, but the miQC object is still available in the filtered SingleCellExperiment objects.

  • Download files with SingleCellExperiment objects now use bz2 compression. This means the file sizes will be much smaller, but you may notice slower read times when loading them into R.

  • This release additionally includes community-contributed projects. Community-contributed projects are 10x Genomics single-cell or single-nuclei datasets that have been processed with the ScPCA pipeline. Please refer to the contributions page for more information about community contributions.


  • Downloads for most projects are now available in AnnData format as HDF5 files. Multiplexed samples are not yet supported.

  • The sample metadata found in single_cell_metadata.tsv has been updated to include ontology term ids for age, sex, organism, ethnicity, diagnosis, and tissue location, when available. See the section describing Metadata on the Downloadable Files page.

  • All samples now have an assigned participant_id, which can be found in single_cell_metadata.tsv. Previously, a participant_id was only assigned when multiple samples mapped to the same participant for most projects.

  • All data files now include both the gene expression data and metadata for each sample (e.g., age, sex, organism, ethnicity, diagnosis, and tissue location). For more information on the contents of the data files, see the Single-cell gene expression file contents page.

  • Data files will include cell type annotations provided by submitters when applicable.


  • The README included in your download now contains the following:

    • More information about how to cite the ScPCA Portal (see also: How to Cite).

    • The date your download was packaged (Generated on: {date}) at the top of the file.

  • The root directory of your download will contain the date you accessed and downloaded data from the ScPCA Portal when uncompressed.