Access the Tabula Muris Senis bulk RNA-seq data

Source: R/TabulaMurisSenisBulk.R

Access the bulk RNA-seq data from the Tabula Muris Senis consortium.

TabulaMurisSenisBulk(infoOnly = FALSE)

Arguments

infoOnly

Logical scalar. If TRUE, only print the total size of the files that will be downloaded to and/or retrieved from the cache.

Value

If infoOnly is FALSE, return a SingleCellExperiment object with a single matrix of counts. Otherwise, returns `NULL`.

Details

The data set was downloaded from GEO (accession number GSE132040). The summary statistics from HTSeq-count were combined with the provided sample metadata and included in the colData of the object. In addition, gene annotations from GENCODE vM19 were downloaded and included in the rowRanges of the object.

References

Schaum et al (2019): The murine transcriptome reveals global aging nodes with organ-specific phase and amplitude. bioRxiv doi:10.1101/662254.

The Tabula Muris Consortium (2020): A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 583:590–595.

Author

Charlotte Soneson

Examples

if (interactive()) {
  sce <- TabulaMurisSenisBulk()
}