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Zeisel Brain Reference Single-Cell RNA-Seq Dataset

Source: R/dataDocumentation.R
zeisel_reference_data.Rd

This dataset contains the processed reference dataset from the Zeisel mouse brain data. It has been preprocessed to include log-normalized counts, a cell type column, and PCA results, and is used to benchmark detectAnomaly and calculateReconstructionError against known ground truth.

Usage

zeisel_reference_data

Format

An object of class SingleCellExperiment with 230 rows and 2103 columns.

Source

The Zeisel mouse brain dataset, available through the scRNAseq package.

Details

This dataset underwent the following steps:

  • Loads the Zeisel mouse brain dataset from the scRNAseq package.

  • Performs log normalization using the function logNormCounts from the scuttle package.

  • Renames the level1class column to true_cell_type.

  • Divides the data into a 70

  • Selects highly variable genes (HVGs) using the function getTopHVGs from the scran package, intersected between the reference and query datasets.

  • Performs Principal Component Analysis (PCA) on the reference dataset using the function runPCA from the scater package.

References

Zeisel A, et al. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347(6226):1138-42.

See also

Use data("zeisel_reference_data") to load and access the resulting reference dataset, and data("zeisel_query_data") for the corresponding query dataset.

Examples

# Load and explore the Zeisel reference dataset
data("zeisel_reference_data")