ZeiselNervousData: Obtain the Zeisel nervous system data

In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

Obtain the Zeisel nervous system data

Description

Obtain the mouse nervous system single-cell RNA-seq dataset from Zeisel et al. (2018).

Usage

ZeiselNervousData(location = TRUE, legacy = FALSE)

Arguments

location	Logical scalar indicating whether genomic coordinates should be returned.
legacy	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

Details

Row data contains the gene symbol as well as some relevant per-gene statistics, e.g., the squared coefficient of variance, mean, and whether it was selected for downstream analyses.

Column data contains a wide variety of fields including patient-level information, sample-level sequencing statistics and many flavors of cell type classification. Note that many numeric columns may have NA values if they could not be successfully parsed form the source file.

If location=TRUE, the coordinates of the Ensembl gene models are stored in the rowRanges of the output.

All data are downloaded from ExperimentHub and cached for local re-use. Specific resources can be retrieved by searching for scRNAseq/zeisel-nervous.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Zeisel A et al. (2018). Molecular architecture of the mouse nervous system. Cell 174(4), 999-1014.

Examples

if (.Machine$sizeof.pointer > 4) { # too large for 32-bit machines!
    sce <- ZeiselNervousData()
}

LTLA/scRNAseq documentation built on June 28, 2024, 7:31 p.m.