R/RNASeqR_package.R

In RNASeqR: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

#' RNASeqR-package
#'
#' @name RNASeqR
#' @importFrom Rsamtools asBam
#' @importFrom clusterProfiler bitr enrichGO groupGO dotplot emapplot
#'   cnetplot goplot enrichKEGG gseGO gseaplot gseKEGG
#' @importFrom pathview pathview
#' @import DOSE
#' @import ggplot2
#' @import graphics
#' @import utils
#' @import grDevices
#' @import methods
#' @import org.Hs.eg.db
#' @import org.Sc.sgd.db
#' @importFrom parallel mcmapply
#' @importFrom tools file_ext
#' @importFrom reticulate py_available py_config
#' @importFrom systemPipeRdata genWorkenvir
#' @importFrom systemPipeR systemArgs seeFastq infile1 seeFastqPlot
#' @importFrom Biostrings quality width
#' @importFrom ballgown ballgown texpr indexes stattest gexpr
#' @importFrom DESeq2 DESeqDataSetFromMatrix DESeq results counts
#'   plotMA plotDispEsts
#' @importFrom edgeR DGEList calcNormFactors estimateCommonDisp
#'   estimateTagwiseDisp exactTest cpm plotMDS.DGEList plotMeanVar plotBCV
#' @importFrom stats t.test quantile cor
#' @importFrom stringr str_extract
#' @importFrom gridExtra grid.table
#' @importFrom rafalib mypar
#' @importFrom reshape2 melt
#' @importFrom FactoMineR PCA
#' @importFrom factoextra get_eigenvalue fviz_eig fviz_pca_ind
#' @importFrom corrplot corrplot
#' @importFrom PerformanceAnalytics chart.Correlation
#' @importFrom pheatmap pheatmap
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