View source: R/BuettnerESCData.R
BuettnerESCData | R Documentation |
Obtain the mouse embryonic stem cell single-cell RNA-seq data from Buettner et al. (2015).
BuettnerESCData(remove.htseq = TRUE, location = TRUE, legacy = FALSE)
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. |
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.
sce <- BuettnerESCData()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.