R/data.R

In tidySingleCellExperiment: Brings SingleCellExperiment to the Tidyverse

#' pbmc_small
#'
#' PBMC single cell RNA-seq data in SingleCellExperiment format
#'
#' @format  A SingleCellExperiment object containing 80 Peripheral Blood 
#'          Mononuclear Cells (PBMC) from 10x Genomics. Generated by subsampling the PBMC dataset of 2,700 single cells.
#' @source \url{https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html}
#' @usage data(pbmc_small)
"pbmc_small"

#' Cell types of 80 PBMC single cells
#' 
#' A dataset containing the barcodes and cell types of 80 PBMC single cells.
#'
#' @format  A tibble containing 80 rows and 2 columns. Cells are a subsample of 
#'          the Peripheral Blood Mononuclear Cells (PBMC) dataset of 2,700 single 
#'          cell. Cell types were identified with SingleR.
#' \describe{
#'   \item{cell}{cell identifier, barcode}
#'   \item{first.labels}{cell type}
#' }
#' @source \url{https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html}
#' @usage data(cell_type_df)
"cell_type_df"

#' Intercellular ligand-receptor interactions for 38 ligands from a single cell RNA-seq cluster.
#'
#' A dataset containing ligand-receptor interactions withibn a sample. There are 38 ligands from a single cell cluster versus 
#' 35 receptors in 6 other clusters.
#'
#' @format  A tibble containing 100 rows and 9 columns. Cells are a subsample of 
#'         the PBMC dataset of 2,700 single cells. Cell interactions were identified with SingleCellSignalR.
#' \describe{
#'   \item{sample}{sample identifier}
#'   \item{ligand}{cluster and ligand identifier}
#'   \item{receptor}{cluster and receptor identifier}
#'   \item{ligand.name}{ligand name}
#'   \item{receptor.name}{receptor name}
#'   \item{origin}{cluster containing ligand}
#'   \item{destination}{cluster containing receptor}
#'   \item{interaction.type}{type of interation, paracrine or autocrine}
#'   \item{LRscore}{interaction score}
#' }
#' @source \url{https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html}
#' @usage data(pbmc_small_nested_interactions)
"pbmc_small_nested_interactions"