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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(checkRLE)
export(createResTable)
export(extractFilteredDESeqResults)
export(fitGlmQL)
export(fitVoomLm)
export(generateSampleTable)
export(generateVolcanoPlot)
export(getTopNGenes)
export(getVoomByGroup)
export(ggplotMDS)
export(gseaDotplot_joint)
export(gseaDotplot_single)
export(heatmapFromGenelist)
export(mappingBinsPlot)
export(normalizeCountsForHeatmap)
export(normalizeCountsForHeatmapByIndividual)
export(parseReadPerGeneFiles)
export(pcaPlotSimple)
export(plotFilterByExpr)
export(plotGeneExpression)
export(plotPCAFromConfig)
export(plotVoomByGroup)
export(read_excel_allsheets)
export(runfgsea)
export(voomByGroup)
export(writeCountTables)
export(writeDESeqResults)
export(writefGSEAResults)
import(ComplexHeatmap)
import(DESeq2)
import(EnhancedVolcano)
import(SummarizedExperiment)
import(dplyr)
import(ggplot2)
import(ggrepel)
import(openxlsx)
importFrom(Biobase,exprs)
importFrom(Biobase,fData)
importFrom(Biobase,pData)
importFrom(DESeq2,counts)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(circlize,colorRamp2)
importFrom(edgeR,voomLmFit)
importFrom(fgsea,fgsea)
importFrom(forcats,fct_inorder)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,title)
importFrom(grid,gpar)
importFrom(here,here)
importFrom(limma,contrasts.fit)
importFrom(limma,decideTests)
importFrom(limma,eBayes)
importFrom(limma,plotMDS)
importFrom(limma,plotSA)
importFrom(magrittr,"%>%")
importFrom(matrixStats,colSums2)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMeans2)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowMins)
importFrom(matrixStats,rowVars)
importFrom(methods,is)
importFrom(methods,new)
importFrom(plyr,mapvalues)
importFrom(readr,read_tsv)
importFrom(readr,write_csv)
importFrom(readr,write_lines)
importFrom(readr,write_tsv)
importFrom(rlang,.data)
importFrom(scales,log_breaks)
importFrom(scales,trans_new)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,prcomp)
importFrom(stringr,str_count)
importFrom(stringr,str_remove)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_to_title)
importFrom(stringr,str_wrap)
importFrom(tibble,as_tibble)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,pivot_longer)
importFrom(utils,head)
importFrom(utils,stack)