Seurat objects now available in results buckets

[jashapiro]

We recently made Seurat files available for the processed objects that are available from the OpenScPCA portal. While the Seurat objects are not directly available for download from the portal, they can be obtained from the project results bucket using the download-results.py script.

For example, to download the Seurat objects for the SCPCP000001 project, you can run the following command (though note you may want to use the --dryrun flag first to see what will be downloaded):

./download-results.py --modules seurat-conversion --project SCPCP000001

Note that the above command does require you to be logged into an AWS account with appropriate access privileges. Test data that does not require login is available by adding the --test-data flag.

For more details on options available in the download-results.py script, see the script documentation

The Seurat objects include the same content as the SingleCellExperiment objects that they are derived from, formatted as Seurat v5 assays.

• These data include raw and normalized counts, annotations of highly variable genes, PCA and UMAP transformations, as well as cell and feature metadata, each of which should be found in slots named according to the Seurat defaults.
• To be more consistent with common Seurat analysis pipelines, these objects use gene symbols rather than Ensembl ids as the row names and primary feature id.
• Note that all calculations were performed using Bioconductor packages, so values will differ from the results obtained using Seurat functions from the same raw data.
  • If your analysis requires additional fields created from Seurat processing pipelines, or you want to compare your results to existing data processed with Seurat, you may need to repeat those processing steps.

The code used to perform the conversions can be found in the seurat-conversion analysis module.