BuettnerESCData: Obtain the Buettner ESC data

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

Obtain the Buettner ESC data

Description

Obtain the mouse embryonic stem cell single-cell RNA-seq data from Buettner et al. (2015).

Usage

BuettnerESCData(remove.htseq = TRUE, location = TRUE, legacy = FALSE)

Arguments

remove.htseq	Logical scalar indicating whether HT-seq alignment statistics should be removed.
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

Rows corresponding to HT-seq's alignment statistics are removed by default. These can be retained by setting remove.htseq=FALSE.

Column metadata contains the experimentally determined cell cycle phase for each cell.

Counts for ERCC spike-ins are stored in the "ERCC" entry in the altExps.

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/buettner-esc.

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Buettner F et al. (2015). Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol. 33(2), 155-160.

Examples

sce <- BuettnerESCData()

LTLA/scRNAseq documentation built on April 24, 2024, 5:58 p.m.