R/MMAPPR2.R

In MMAPPR2: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

#' Mutation Mapping Analysis Pipeline for Pooled RNA-seq
#'
#' The main functionality of this package is described in the \code{\link{mmappr}}
#' function.
#'
#' @docType package
#' @name MMAPPR2
#'
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#' @import methods
#' @importFrom magrittr %>%
#' @importFrom graphics abline mtext par plot polygon axis legend
#' @importFrom grDevices dev.off dev.list pdf rgb graphics.off
#' @importFrom stats approxfun density.default loess median var
#' @importFrom utils capture.output object.size str write.table tail sessionInfo
#' @importFrom gmapR GmapGenome
#' @importFrom ensemblVEP VEPFlags
#' @importFrom Rsamtools BamFileList mergeBam
#' @importFrom VariantTools TallyVariantsParam callVariants
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