MouseRNAseqData {SingleR} | R Documentation |
Download and cache the normalized expression values of 358 bulk RNA-seq samples of sorted cell populations that can be found at GEO.
MouseRNAseqData(ensembl = FALSE)
ensembl |
Logical scalar indicating whether to convert row names to Ensembl IDs. Genes without a mapping to a non-duplicated Ensembl ID are discarded. |
This dataset was contributed by the Benayoun Lab that identified, downloaded and processed data sets on GEO that corresponded to sorted cell types (Benayoun et al., 2019).
The dataset contains 358 mouse RNA-seq samples annotated to 18 main cell types:
Adipocytes
Astrocytes
B cells
Cardiomyocytes
Dendritic cells
Endothelial cells
Epithelial cells
Erythrocytes
Fibroblasts
Granulocytes
Hepatocytes
Macrophages
Microglia
Monocytes
Neurons
NK cells
Oligodendrocytes
T cells
A SummarizedExperiment object with a "logcounts"
assay
containing the log-normalized expression values, along with cell type labels in the
colData
.
Friederike Dündar
Benayoun B et al. (2019). Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses. Genome Res. 29, 697-709.
ref.se <- MouseRNAseqData()