R/flowSpecs-package.R

In flowSpecs: Tools for processing of high-dimensional cytometry data

#' Tools for processing high-dimensional cytometry files
#'
#' @description This package is intended to fill the role of conventional
#' cytometry pre-processing software, for spectral decomposition,
#' transformation, visualization and cleanup, and to aid further downstream
#' analyses, such as with DepecheR, by enabling transformation of flowFrames
#' and flowSets to dataframes. Functions for flowCore-compliant automatic
#' 1D-gating/filtering are in the pipe line.
#' It is worth noting here that even if there are dedicated spectral cytometers,
#' it is possible to increase the separation of the fluorochromes in a
#' conventional flow cytometer too, by just keeping all non-used channels open.
#' That will however also require the use of spectral unmixing, rather than
#' compensation, as the compensation functions generally require the
#' compensation matrix to be symmetrical. So please open all channels, and use
#' this software!
#'
#' @name flowSpecs-package
#' @aliases flowSpecs-package flowSpecs
#' @docType package
#' @author
#' Maintainer: Jakob Theorell <jakob.theorell@@ndcn.ox.ac.uk>
#' @seealso \code{\link[flowCore:flowCore-package]{flowCore}}
#' @keywords package
#' @importFrom stats density lsfit mad median quantile
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