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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(KallistoExperiment)
export(annotateFeatures)
export(calcTpm)
export(collapseBundles)
export(collapseByTss)
export(collapseTpm)
export(collapseTranscripts)
export(crossModels)
export(eff_length)
export(extractIndexName)
export(fastqFileUploadToBaseSpace)
export(fetchAppSession)
export(fetchKallisto)
export(fitBundles)
export(fitRepeats)
export(fitTranscripts)
export(geneWiseAnalysis)
export(getKallistoVersion)
export(indexKallisto)
export(kallistoVersion)
export(mabDev)
export(mergeKallisto)
export(pairFastqFiles)
export(parseFastqNames)
export(remapSymbols)
export(repeatWiseAnalysis)
export(rpkmToTpm)
export(runKallisto)
export(ruvNormalization)
export(showTnxBundles)
export(sraFastqHeaderToIlluminaStandard)
export(tpm)
export(transcriptWiseAnalysis)
export(transcriptomes)
exportClasses(KallistoExperiment)
exportMethods(eff_length)
exportMethods(kallistoVersion)
exportMethods(mabDev)
exportMethods(pData)
exportMethods(tpm)
exportMethods(transcriptomes)
import(BiocGenerics)
import(ComplexHeatmap)
import(GenomicRanges)
import(circlize)
import(rhdf5)
import(tools)
importFrom(EDASeq,plotPCA)
importFrom(EDASeq,plotRLE)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInGroup)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,transcripts)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,promoters)
importFrom(IRanges,reduce)
importFrom(RUVSeq,RUVg)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(TxDbLite,createAnnotationPackage)
importFrom(TxDbLite,findDupes)
importFrom(TxDbLite,getAnnotationType)
importFrom(TxDbLite,getFastaStub)
importFrom(TxDbLite,getOrgDetails)
importFrom(TxDbLite,getSupportedAbbreviations)
importFrom(TxDbLite,getTxDbLiteName)
importFrom(TxDbLite,strpop)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useMart)
importFrom(dendsort,dendsort)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateGLMCommonDisp)
importFrom(edgeR,estimateGLMRobustDisp)
importFrom(edgeR,estimateGLMTagwiseDisp)
importFrom(edgeR,estimateGLMTrendedDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,plotBCV)
importFrom(edgeR,topTags)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,title)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(jsonlite,fromJSON)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,volcanoplot)
importFrom(limma,voom)
importFrom(matrixStats,rowMads)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowSds)
importFrom(nat.utils,is.gzip)
importFrom(parallel,mclapply)
importFrom(pvclust,pvclust)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(utils,data)
importFrom(utils,read.delim)
importFrom(utils,write.csv)
importFrom(utils,write.table)