LengESCData: Obtain the Leng ESC data

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

Obtain the Leng ESC data

Description

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

Usage

LengESCData(ensembl = FALSE, location = TRUE, legacy = FALSE)

Arguments

ensembl	Logical scalar indicating whether gene symbols should be converted to Ensembl annotation.
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 contains the cell line, experiment number and experimentally determined cell cycle phase for each cell.

If ensembl=TRUE, the gene symbols in the published annotation are converted to Ensembl. 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/leng-esc.

Value

A SingleCellExperiment object with a single matrix of normalized expected read counts.

Author(s)

Aaron Lun

References

Leng F et al. (2015). Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nat. Methods 12(10), 947-950.

Examples

sce <- LengESCData()

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