BuettnerESCData: Obtain the Buettner ESC data
In drisso/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

Description Usage Arguments Details Value Author(s) References Examples

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

1	BuettnerESCData(remove.htseq = TRUE, location = TRUE)

`remove.htseq`	Logical scalar indicating whether HT-seq alignment statistics should be removed.
`location`	Logical scalar indicating whether genomic coordinates should be returned.

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.

A SingleCellExperiment object with a single matrix of read counts.

Aaron Lun

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.