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. 2025 Jun 2;13:1256. Originally published 2024 Oct 21. [Version 2] doi: 10.12688/f1000research.154675.2

Figure 2. The methods added by SCUBA simplify the retrieval of data from supported object classes.

Figure 2.

The existing Seurat method (first column), is compared to the methods added by SCUBA for SingleCellExperiment and anndata objects (second and third columns). The methods use consistent syntax across object classes and involve the use of only a few parameters. Pseudocode is used in the examples. object represents a single-cell object. features represents one or more features, from any modality in the object. metadata represents one or more metadata variables, for example, cell type classifications. reduction_dims represents a set of dimensions in a reduction included with the object, with the number of the dimension separated from the reduction with an underscore. For example, to fetch the first and second dimensions of the UMAP projection, reduction_dims would be c(“UMAP_1”, “UMAP_2”).