R/CascadeData-package.R

In CascadeData: Experimental Data of Cascade Experiments in Genomics

#' Experimental Data of Cascade Experiments in Genomics
#' 
#' These are the data from the agressive subject group the from GSE39411
#' dataset, \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39411},
#' Vallat, L., Kemper, C. A., Jung, N., Maumy-Bertrand, M., Bertrand, F.,
#' \dots{}, Bahram, S. (2013). Reverse-engineering the genetic circuitry of a
#' cancer cell with predicted intervention in chronic lymphocytic leukemia.
#' Proceedings of the National Academy of Sciences, 110(2), 459-464,
#' \doi{10.1073/pnas.1211130110}
#' 
#' 5 leukemic CLL B-lymphocyte of aggressive form were stimulated in vitro with
#' an anti-IgM antibody, activating the B-cell receptor (BCR). We analyzed the
#' gene expression at 4 time points (60, 90, 210 and 390 minutes). Each gene
#' expression measurement is performed both in stimulated cells and in control
#' unstimulated cells.
#' 
#' The data were normalized and are ready to use.
#' 
#' These Experimental Data are used as examples by packages such as the Cascade
#' one \doi{10.1093/bioinformatics/btt705} in one of its vignettes. The Cascade
#' package is a modeling tool allowing gene selection, reverse engineering, and
#' prediction in Cascade networks.
#' 
#' Data were collected on HG-U133_Plus_2, Affymetrix Human Genome U133 Plus 2.0
#' Array.
#' 
#' @name CascadeData-package
#' @aliases CascadeData-package CascadeData
#' @docType package
#' @author This package has been written by Frederic Bertrand, Myriam
#' Maumy-Bertrand and Nicolas Jung with biological insights from Laurent
#' Vallat.
#' 
#' Maintainer: Frederic Bertrand <frederic.bertrand@@utt.fr>
#' @references Jung, N., Bertrand, F., Bahram, S., Vallat, L., and
#' Maumy-Bertrand, M. (2013). Cascade: a R-package to study, predict and
#' simulate the diffusion of a signal through a temporal gene network.
#' \emph{Bioinformatics}, btt705.
#' 
#' Vallat, L., Kemper, C. A., Jung, N., Maumy-Bertrand, M., Bertrand, F., ... &
#' Bahram, S. (2013). Reverse-engineering the genetic circuitry of a cancer
#' cell with predicted intervention in chronic lymphocytic leukemia.
#' \emph{Proceedings of the National Academy of Sciences}, 110(2), 459-464.
#' @keywords package
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