KolodziejczykESCData: Obtain the Kolodziejcyzk ESC data

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

Obtain the Kolodziejcyzk ESC data

Description

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

Usage

KolodziejczykESCData(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

Column metadata is generated from the column names, and contains the culture conditions and the plate of origin for each cell.

Count data 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/kolodziejczyk-esc.

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Messmer T et al. (2019). Transcriptional heterogeneity in naive and primed human pluripotent stem cells at single-cell resolution. Cell Rep 26(4), 815-824.e4

Examples

sce <- KolodziejczykESCData()

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