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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("sampleInfo<-")
export(annotateTSS)
export(demultiplexFASTQ)
export(detectDiffTSS)
export(detectTSS)
export(exampleCSobject)
export(filterDuplicates)
export(fitDiffTSS)
export(getGeneCounts)
export(getNormFactors)
export(mapCaps)
export(newCapSet)
export(plotReadStats)
export(plotTSSprecision)
export(sampleInfo)
export(splitBAM_byIndex)
export(splitBAM_byRepindex)
exportMethods("sampleInfo<-")
exportMethods(demultiplexFASTQ)
exportMethods(detectDiffTSS)
exportMethods(detectTSS)
exportMethods(exportTSS)
exportMethods(filterDuplicates)
exportMethods(fitDiffTSS)
exportMethods(getGeneCounts)
exportMethods(getNormFactors)
exportMethods(plotReadStats)
exportMethods(plotTSSprecision)
exportMethods(sampleInfo)
import(TxDb.Dmelanogaster.UCSC.dm6.ensGene)
importClassesFrom(S4Vectors,DataFrame)
importFrom(BiocGenerics,width)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SnowParam)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,quality)
importFrom(DESeq2,results)
importFrom(GenomicAlignments,summarizeOverlaps)
importFrom(GenomicFeatures,transcriptsBy)
importFrom(GenomicRanges,tileGenome)
importFrom(IRanges,narrow)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,countBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,sortBam)
importFrom(S4Vectors,aggregate)
importFrom(ShortRead,sread)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"mcols<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,mcols)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VariantAnnotation,AllVariants)
importFrom(VariantAnnotation,PromoterVariants)
importFrom(VariantAnnotation,locateVariants)
importFrom(csaw,filterWindows)
importFrom(csaw,mergeWindows)
importFrom(csaw,readParam)
importFrom(csaw,regionCounts)
importFrom(csaw,strandedCounts)
importFrom(edgeR,glmQLFTest)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,stat_ecdf)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_gray)
importFrom(ggplot2,theme_light)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,smoothScatter)
importFrom(limma,makeContrasts)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,validObject)
importFrom(rtracklayer,export.bed)
importFrom(stats,model.matrix)
importFrom(stats,reshape)
importFrom(utils,capture.output)
importFrom(utils,write.table)