Processed single-cell RNA-seq cell-cycle data

A processed representation of the single-cell RNA-seq data from Buettner et al. (2015). The object holds 182 mouse embryonic stem cells, one cell-cycle label per cell, and 8,989 numeric feature columns. Feature names are positional because the preprocessing script that produced this object is no longer available.

Usage

data_cell_cycle

Format

A tibble with 182 rows and 8,990 columns:

Cell_cycle

Character cell-cycle label, one of G1, S, or G2M.

1–8989

Numeric processed RNA-seq features.

Source

ArrayExpress accession E-MTAB-2805.

Details

Rows are stored in label order: 1 to 59 are G1, 60 to 117 are S, and 118 to 182 are G2M.

References

Buettner F, Natarajan KN, Casale FP, et al. (2015). Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature Biotechnology, 33, 155–160. doi:10.1038/nbt.3102 .

Examples

data(data_cell_cycle, package = "PreciseDist")

table(data_cell_cycle$Cell_cycle)
#> 
#>  G1 G2M   S 
#>  59  65  58 

cells <- c(1:4, 60:63, 118:121)
cell_cycle <- as.matrix(data_cell_cycle[cells, 2:41])
rownames(cell_cycle) <- paste0(data_cell_cycle$Cell_cycle[cells], "_", cells)
dim(cell_cycle)
#> [1] 12 40