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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(fit,OutriderDataSet)
export("counts<-")
export("normalizationFactors<-")
export("sampleExclusionMask<-")
export("sizeFactors<-")
export(OUTRIDER)
export(OutriderDataSet)
export(aberrant)
export(computeGeneLength)
export(computeLatentSpace)
export(controlForConfounders)
export(counts)
export(dispersions)
export(estimateBestQ)
export(estimateSizeFactors)
export(filterExpression)
export(findEncodingDim)
export(findInjectZscore)
export(fit)
export(fpkm)
export(fpm)
export(getBestQ)
export(makeExampleOutriderDataSet)
export(normalizationFactors)
export(pValue)
export(padj)
export(plotAberrantPerSample)
export(plotCountCorHeatmap)
export(plotCountGeneSampleHeatmap)
export(plotDispEsts)
export(plotEncDimSearch)
export(plotExpectedVsObservedCounts)
export(plotExpressedGenes)
export(plotExpressionRank)
export(plotFPKM)
export(plotManhattan)
export(plotPowerAnalysis)
export(plotQQ)
export(plotSizeFactors)
export(plotVolcano)
export(results)
export(sampleExclusionMask)
export(sizeFactors)
export(theta)
export(zScore)
exportMethods(aberrant)
exportMethods(computePvalues)
exportMethods(computeZscores)
exportMethods(dispersions)
exportMethods(filterExpression)
exportMethods(plotAberrantPerSample)
exportMethods(plotCountCorHeatmap)
exportMethods(plotDispEsts)
exportMethods(plotEncDimSearch)
exportMethods(plotManhattan)
exportMethods(plotQQ)
exportMethods(plotVolcano)
exportMethods(results)
import(data.table, except=melt)
import(methods)
importFrom(BBmisc,chunk)
importFrom(BBmisc,isFALSE)
importFrom(BBmisc,isScalarCharacter)
importFrom(BBmisc,isScalarLogical)
importFrom(BBmisc,isScalarNA)
importFrom(BBmisc,isScalarNumeric)
importFrom(BBmisc,isScalarValue)
importFrom(BBmisc,seq_col)
importFrom(BBmisc,seq_row)
importFrom(BiocGenerics,estimateSizeFactors)
importFrom(BiocGenerics,plotDispEsts)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bpisup)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpparam)
importFrom(BiocParallel,bpstart)
importFrom(BiocParallel,bpstop)
importFrom(DESeq2,"counts<-")
importFrom(DESeq2,"normalizationFactors<-")
importFrom(DESeq2,"sizeFactors<-")
importFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,dispersions)
importFrom(DESeq2,estimateSizeFactorsForMatrix)
importFrom(DESeq2,fpkm)
importFrom(DESeq2,fpm)
importFrom(DESeq2,makeExampleDESeqDataSet)
importFrom(DESeq2,normalizationFactors)
importFrom(DESeq2,plotDispEsts)
importFrom(DESeq2,replaceOutliers)
importFrom(DESeq2,show)
importFrom(DESeq2,sizeFactors)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,makeTxDbFromGFF)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(PRROC,pr.curve)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,"values<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,values)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"mcols<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,mcols)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(generics,fit)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,quo_name)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_identity)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,box)
importFrom(graphics,grid)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(heatmaply,heatmaply)
importFrom(matrixStats,rowCumsums)
importFrom(matrixStats,rowMeans2)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowQuantiles)
importFrom(matrixStats,rowSds)
importFrom(pcaMethods,loadings)
importFrom(pcaMethods,pca)
importFrom(pheatmap,pheatmap)
importFrom(plotly,"%>%")
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plotly,plotly_build)
importFrom(plyr,.)
importFrom(reshape2,melt)
importFrom(scales,math_format)
importFrom(scales,trans_format)
importFrom(splines,bs)
importFrom(stats,Gamma)
importFrom(stats,coefficients)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,dnbinom)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,optim)
importFrom(stats,optimize)
importFrom(stats,p.adjust)
importFrom(stats,pnbinom)
importFrom(stats,ppoints)
importFrom(stats,predict)
importFrom(stats,qbeta)
importFrom(stats,quantile)
importFrom(stats,rlnorm)
importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(utils,compareVersion)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
useDynLib(OUTRIDER)