# Generated by roxygen2: do not edit by hand

export(buildSummarized)
export(diag_plots)
export(multi_de_pairs)
import(BiocGenerics)
import(Biostrings)
import(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
import(airway)
importFrom(AnnotationDbi,columns)
importFrom(AnnotationDbi,keytypes)
importFrom(AnnotationDbi,mapIds)
importFrom(Biobase,pData)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,register)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,counts)
importFrom(DESeq2,results)
importFrom(EDASeq,"normCounts<-")
importFrom(EDASeq,betweenLaneNormalization)
importFrom(EDASeq,newSeqExpressionSet)
importFrom(EDASeq,normCounts)
importFrom(EDASeq,plotRLE)
importFrom(GenomicAlignments,invertStrand)
importFrom(GenomicAlignments,summarizeOverlaps)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,makeTxDbFromGFF)
importFrom(GenomicFeatures,transcriptsBy)
importFrom(RColorBrewer,brewer.pal)
importFrom(RUVSeq,RUVr)
importFrom(Rsamtools,BamFileList)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(data.table,fread)
importFrom(dendextend,"%>%")
importFrom(dendextend,colored_bars)
importFrom(dendextend,set)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,estimateGLMCommonDisp)
importFrom(edgeR,estimateGLMTagwiseDisp)
importFrom(edgeR,filterByExpr)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,topTags)
importFrom(ensembldb,transcripts)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(pcaMethods,R2cum)
importFrom(pcaMethods,pca)
importFrom(pcaMethods,prep)
importFrom(pcaMethods,scores)
importFrom(stats,as.dendrogram)
importFrom(utils,read.table)
