R/data.R

In satijalab/seurat: Tools for Single Cell Genomics

#' Cell cycle genes
#'
#' A list of genes used in cell-cycle regression
#'
#' @format A list of two vectors
#' \describe{
#'   \item{s.genes}{Genes associated with S-phase}
#'   \item{g2m.genes}{Genes associated with G2M-phase}
#' }
#' @concept data
#' @source \url{https://www.science.org/doi/abs/10.1126/science.aad0501}
#'
"cc.genes"

#' Cell cycle genes: 2019 update
#'
#' A list of genes used in cell-cycle regression, updated with 2019 symbols
#'
#' @section Updated symbols:
#' The following symbols were updated from \code{\link{cc.genes}}
#' \describe{
#'   \item{s.genes}{
#'     \itemize{
#'       \item \emph{MCM2}: \emph{MCM7}
#'       \item \emph{MLF1IP}: \emph{CENPU}
#'       \item \emph{RPA2}: \emph{POLR1B}
#'       \item \emph{BRIP1}: \emph{MRPL36}
#'     }
#'   }
#'   \item{g2m.genes}{
#'     \itemize{
#'       \item \emph{FAM64A}: \emph{PIMREG}
#'       \item \emph{HN1}: \emph{JPT1}
#'     }
#'   }
#' }
#'
#' @format A list of two vectors
#' \describe{
#'   \item{s.genes}{Genes associated with S-phase}
#'   \item{g2m.genes}{Genes associated with G2M-phase}
#' }
#' @concept data
#' @source \url{https://www.science.org/doi/abs/10.1126/science.aad0501}
#'
#' @seealso \code{\link{cc.genes}}
#'
#' @examples
#' \dontrun{
#' cc.genes.updated.2019 <- cc.genes
#' cc.genes.updated.2019$s.genes <- UpdateSymbolList(symbols = cc.genes.updated.2019$s.genes)
#' cc.genes.updated.2019$g2m.genes <- UpdateSymbolList(symbols = cc.genes.updated.2019$g2m.genes)
#' }
#'
"cc.genes.updated.2019"