MessmerESCData: Obtain the Messmer ESC data

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

Obtain the Messmer ESC data

Description

Obtain the human embryonic stem cell single-cell RNA-seq data from Messmer et al. (2019).

Usage

MessmerESCData(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 a single "Length" field describing the total exonic length of each feature.

Column metadata is provided in the same form as supplied in E-MTAB-6819. This contains information such as the cell phenotype (naive or primed) and the batch of origin. Note that counts for technical replicates have already been summed together.

Count data for ERCC spike-ins are stored in the "ERCC" entry of 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/messmer-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 <- MessmerESCData()

LTLA/scRNAseq documentation built on April 19, 2024, 10:36 a.m.