# Generated by roxygen2: do not edit by hand

export(alphaSummary)
export(download)
export(ggplot)
export(inferno)
export(loadRNASeq)
export(loadRNASeqRun)
export(meltLog10)
export(plot53Bias)
export(plotCorrelationHeatmap)
export(plotCountDensity)
export(plotCountsPerGene)
export(plotDEGHeatmap)
export(plotDispersion)
export(plotExonicMappingRate)
export(plotGenderMarkers)
export(plotGeneDetectionSaturation)
export(plotGeneHeatmap)
export(plotGeneSaturation)
export(plotGenesDetected)
export(plotHeatmap)
export(plotIntronicMappingRate)
export(plotMappedReads)
export(plotMappingRate)
export(plotMeanSD)
export(plotPCACovariates)
export(plotRRNAMappingRate)
export(plotTotalReads)
export(plotVolcano)
export(prepareRNASeqTemplate)
export(resultsTables)
export(scale_color_viridis)
export(scale_fill_viridis)
export(tmm)
export(topTables)
export(tpm)
export(txi)
export(viridis)
exportClasses(bcbioRNADataSet)
exportClasses(bcbioRNASeq)
exportMethods("[")
exportMethods("bcbio<-")
exportMethods("interestingGroups<-")
exportMethods(aggregateReplicates)
exportMethods(alphaSummary)
exportMethods(annotable)
exportMethods(bcbio)
exportMethods(counts)
exportMethods(flatFiles)
exportMethods(interestingGroups)
exportMethods(meltLog10)
exportMethods(metrics)
exportMethods(plot53Bias)
exportMethods(plotCorrelationHeatmap)
exportMethods(plotCountDensity)
exportMethods(plotCountsPerGene)
exportMethods(plotDEGHeatmap)
exportMethods(plotDispEsts)
exportMethods(plotExonicMappingRate)
exportMethods(plotGenderMarkers)
exportMethods(plotGene)
exportMethods(plotGeneSaturation)
exportMethods(plotGenesDetected)
exportMethods(plotHeatmap)
exportMethods(plotIntronicMappingRate)
exportMethods(plotMA)
exportMethods(plotMappedReads)
exportMethods(plotMappingRate)
exportMethods(plotMeanSD)
exportMethods(plotPCA)
exportMethods(plotPCACovariates)
exportMethods(plotRRNAMappingRate)
exportMethods(plotTotalReads)
exportMethods(plotVolcano)
exportMethods(prepareRNASeqTemplate)
exportMethods(resultsTables)
exportMethods(sampleMetadata)
exportMethods(tmm)
exportMethods(topTables)
exportMethods(tpm)
exportMethods(txi)
import(SummarizedExperiment)
import(methods)
importClassesFrom(DESeq2,DESeqDataSet)
importClassesFrom(DESeq2,DESeqTransform)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,density)
importFrom(BiocGenerics,design)
importFrom(BiocGenerics,plotDispEsts)
importFrom(BiocGenerics,plotMA)
importFrom(BiocGenerics,plotPCA)
importFrom(DEGreport,degCovariates)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,DESeqDataSetFromTximport)
importFrom(DESeq2,DESeqTransform)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,results)
importFrom(DESeq2,rlog)
importFrom(DESeq2,varianceStabilizingTransformation)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,cor)
importFrom(S4Vectors,head)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,na.omit)
importFrom(basejump,"bcbio<-")
importFrom(basejump,"interestingGroups<-")
importFrom(basejump,aggregateReplicates)
importFrom(basejump,annotable)
importFrom(basejump,bcbio)
importFrom(basejump,camel)
importFrom(basejump,checkInterestingGroups)
importFrom(basejump,detectOrganism)
importFrom(basejump,fixNA)
importFrom(basejump,flatFiles)
importFrom(basejump,interestingGroups)
importFrom(basejump,metrics)
importFrom(basejump,plotGene)
importFrom(basejump,prepareSummarizedExperiment)
importFrom(basejump,sampleMetadata)
importFrom(basejump,snake)
importFrom(basejump,uniteInterestingGroups)
importFrom(cowplot,draw_plot)
importFrom(cowplot,ggdraw)
importFrom(cowplot,plot_grid)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,mutate_if)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select_if)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(ggplot2,aes_)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotation_logticks)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grid,arrow)
importFrom(grid,unit)
importFrom(knitr,kable)
importFrom(magrittr,"%>%")
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_rownames)
importFrom(pheatmap,pheatmap)
importFrom(readr,read_csv)
importFrom(readr,read_tsv)
importFrom(readr,write_csv)
importFrom(reshape2,melt)
importFrom(rlang,"!!!")
importFrom(rlang,"!!")
importFrom(rlang,.data)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(stats,formula)
importFrom(stats,setNames)
importFrom(stringr,str_match)
importFrom(tibble,column_to_rownames)
importFrom(tibble,remove_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,unite)
importFrom(tximport,tximport)
importFrom(utils,capture.output)
importFrom(utils,globalVariables)
importFrom(utils,packageVersion)
importFrom(viridis,inferno)
importFrom(viridis,scale_color_viridis)
importFrom(viridis,scale_fill_viridis)
importFrom(viridis,viridis)
importFrom(vsn,meanSdPlot)
