R/allenpvc.R

In diogo-branco/allenpvc: GEO accession data GSE71585 as a SingleCellExperiment

#' Adult mouse cortical cell taxonomy by single cell transcriptomics
#'
#' Celular taxonomy of the primary visual cortex in adult mice based on single
#' cell RNA-sequencing from a study performed by the Allen Institute for Brain
#' Science. In said study 49 transcriptomic cell types are identified.
#' This data set is the supplementary data from GEO accession
#' \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585}{GSE71585}
#' encapsulated in a \code{\link[SingleCellExperiment]{SingleCellExperiment}}.
#'
#' See the vignette for examples of using these data in differential gene
#' expression analysis.
#'
#' browseVignettes("allenpvc")
#'
#' Details of how this data was created are in the inst/scripts/ directory of
#' the source package.
#'
#' @format The data is encapsulated in a
#' \code{\link[SingleCellExperiment]{SingleCellExperiment}} object available
#' through \code{\link[ExperimentHub]{ExperimentHub}}
#' @source https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585
#' @import AnnotationHub
#' @import ExperimentHub
#' @import SingleCellExperiment
#' @examples
#' allenpvc()
#' @references Tasic, Bosiljka, et al. Adult mouse cortical cell taxonomy
#'     revealed by single cell transcriptomics. Nature neuroscience 19.2 (2016):
#'     335.
#' @export
allenpvc <- function() {
    eh <- ExperimentHub()
    return(eh[["EH1433"]])
}