R/data.R

In johannesnicolaus/ASURAT_source: Assisting Interpretable Classifications in Single-cell Transcriptomics

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#
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#' Single-cell RNA-seq data of human cervix cancer cells
#'
#' This dataset includes small cell neuroendocrine carcinoma, adenocarcinoma,
#' and their combined phenotypes. Quality control was performed to remove cell
#' outliers.
#'
#'
#' The original data was produced by Nx1-seq using unique molecular identifiers
#' (UMIs) from cancer tissue originated spheroids (CTOSs) isolated from cervix
#' cancer patients, followed by in-vitro culture under hypoxic conditions for
#' seven days.
#' The CTOS line, cerv21, was introduced in Kubota et al., BBRC \strong{524},
#' 398-404 (2020). The scRNA-seq data were published in DDBJ under the
#' following accession numbers: DRA007915; DRX155817 and DRX155818.
#'
#' @format An R list consisting of the following items:
#' \describe{
#'   \item{mat_expression}{a numeric matrix with 1012 rows and 515 columns,
#'     of which the row and column names, and entries stand for gene symbols,
#'     cell barcodes, and raw read counts, respectively.}
#'   \item{gene_symbol}{a one-dimensional vector with 1012 elements of
#'     gene symbols, corresponding to the rows of mat_expression.}
#'   \item{gene_entrez}{a one-dimensional vector with 1012 elements of
#'     Entrez gene IDs, corresponding to the rows of mat_expression.}
#'   \item{sample_identity}{a one-dimensional vector with 515 elements of
#'     cell barcodes, corresponding to the columns of mat_expression.}
#' }
"cerv_asurat"
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#' Single-cell RNA-seq data of peripheral blood mononuclear cells (PBMC 4k)
#'
#' Original data "4k PBMCs from a Healthy Donor" downloaded from 10x
#' Genomics database. Quality control was performed to remove cell outliers.
#'
#' @format An R list consisting of the following items:
#' \describe{
#'   \item{mat_expression}{a matrix with 1016 rows and 527 columns,
#'     of which the row and column names, and entries stand for gene symbols,
#'     cell barcodes, and raw read counts, respectively.}
#'   \item{gene_symbol}{a one-dimensional vector with 1016 elements of
#'     gene symbols, corresponding to the rows of mat_expression.}
#'   \item{gene_entrez}{a one-dimensional vector with 1016 elements of
#'     Entrez gene IDs, corresponding to the rows of mat_expression.}
#'   \item{sample_identity}{a one-dimensional vector with 527 elements of
#'     cell barcodes, corresponding to the columns of mat_expression.}
#' }
#' @source \url{https://support.10xgenomics.com/single-cell-gene-expression}
"pbmc_asurat"