R/datasets.R

In carmonalab/UCell: Rank-based signature enrichment analysis for single-cell data

#' Sample dataset to test UCell installation
#'
#' A sparse matrix (class "dgCMatrix") of single-cell transcriptomes
#' (scRNA-seq) for 30 cells and 20729 genes.
#' Single-cell UMI counts were normalized using a standard log-normalization:
#' counts for each cell were divided by the total counts for that cell and
#' multiplied by 10,000, then natural-log transformed using `log1p`. \cr\cr
#' This a subsample of T cells from the
#' large scRNA-seq PBMC dataset published
#' by \href{https://doi.org/10.1016/j.cell.2021.04.048}{Hao et al.} and
#' available as UMI counts at
#' \url{https://atlas.fredhutch.org/data/nygc/multimodal/pbmc_multimodal.h5seurat}
#' 
#' @format A sparse matrix of 30 cells and 20729 genes.
#' @source \url{https://doi.org/10.1016/j.cell.2021.04.048}
"sample.matrix"