# Generated by roxygen2: do not edit by hand

export("assay<-")
export("assayNames<-")
export("assays<-")
export("colData<-")
export("rowData<-")
export(ASEFilter)
export(ASE_DESeq)
export(ASE_DoubleExpSeq)
export(ASE_limma)
export(ASE_satuRn)
export(BAM2COV)
export(STAR_alignExperiment)
export(STAR_alignReads)
export(STAR_buildRef)
export(STAR_mappability)
export(STAR_version)
export(SpliceWiz_example_NxtSE)
export(SpliceWiz_example_bams)
export(applyFilters)
export(as_ggplot_cov)
export(assay)
export(assayNames)
export(assays)
export(buildFullRef)
export(buildRef)
export(calculateMappability)
export(colData)
export(collateData)
export(coord2GR)
export(findBAMS)
export(findFASTQ)
export(findSamples)
export(findSpliceWizOutput)
export(generateSyntheticReads)
export(getCoverage)
export(getCoverageBins)
export(getCoverageRegions)
export(getCoverage_DF)
export(getDefaultFilters)
export(getNonPolyARef)
export(getResources)
export(isCOV)
export(makeMatrix)
export(makeMeanPSI)
export(makeSE)
export(plotCoverage)
export(plotGenome)
export(processBAM)
export(rowData)
export(runFilter)
export(setSWthreads)
export(spliceWiz)
export(theme_white)
export(theme_white_legend)
export(theme_white_legend_plot_track)
export(viewASE)
export(viewExons)
export(viewGenes)
export(viewIR)
export(viewIR_NMD)
export(viewIntrons)
export(viewProteins)
export(viewTranscripts)
exportClasses(ASEFilter)
exportClasses(NxtSE)
exportMethods("[")
exportMethods("[<-")
exportMethods("covfile<-")
exportMethods("down_exc<-")
exportMethods("down_inc<-")
exportMethods("sampleQC<-")
exportMethods("up_exc<-")
exportMethods("up_inc<-")
exportMethods(cbind)
exportMethods(coerce)
exportMethods(covfile)
exportMethods(down_exc)
exportMethods(down_inc)
exportMethods(junc_PSI)
exportMethods(junc_counts)
exportMethods(junc_gr)
exportMethods(rbind)
exportMethods(realize_NxtSE)
exportMethods(ref)
exportMethods(sampleQC)
exportMethods(up_exc)
exportMethods(up_inc)
import(NxtIRFdata)
import(data.table)
import(ggplot2)
import(ompBAM)
import(shiny)
import(shinydashboard)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(AnnotationHub,AnnotationHub)
importFrom(AnnotationHub,cache)
importFrom(BSgenome,getSeq)
importFrom(BiocFileCache,BiocFileCache)
importFrom(BiocFileCache,bfcquery)
importFrom(BiocFileCache,bfcrpath)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,ncol)
importFrom(BiocGenerics,nrow)
importFrom(BiocGenerics,rbind)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,width)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,translate)
importFrom(DT,dataTableProxy)
importFrom(DT,datatable)
importFrom(DT,selectRows)
importFrom(DelayedArray,DelayedArray)
importFrom(DelayedArray,plogis)
importFrom(DelayedArray,qlogis)
importFrom(DelayedArray,rowMeans)
importFrom(DelayedArray,rowSums)
importFrom(DelayedMatrixStats,rowAnyNAs)
importFrom(DelayedMatrixStats,rowMaxs)
importFrom(DelayedMatrixStats,rowSds)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,genomeStyles)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicRanges,"mcols<-")
importFrom(GenomicRanges,"seqnames<-")
importFrom(GenomicRanges,"strand<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,disjoin)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,flank)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,makeGRangesListFromDataFrame)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,psetdiff)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,setdiff)
importFrom(GenomicRanges,split)
importFrom(GenomicRanges,strand)
importFrom(HDF5Array,HDF5Array)
importFrom(HDF5Array,h5writeDimnames)
importFrom(HDF5Array,writeHDF5Array)
importFrom(IRanges,IRanges)
importFrom(IRanges,RleList)
importFrom(IRanges,Views)
importFrom(R.utils,gzip)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(Rcpp,evalCpp)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,bindCOLS)
importFrom(S4Vectors,bindROWS)
importFrom(S4Vectors,from)
importFrom(S4Vectors,getListElement)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,setListElement)
importFrom(S4Vectors,setValidity2)
importFrom(S4Vectors,to)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(XML,getHTMLLinks)
importFrom(fst,read.fst)
importFrom(fst,threads_fst)
importFrom(fst,write.fst)
importFrom(genefilter,rowttests)
importFrom(grDevices,colorRampPalette)
importFrom(heatmaply,heatmaply)
importFrom(magrittr,"%>%")
importFrom(matrixStats,colVars)
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,coerce)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,validObject)
importFrom(parallel,detectCores)
importFrom(pheatmap,pheatmap)
importFrom(plotly,config)
importFrom(plotly,event_data)
importFrom(plotly,ggplotly)
importFrom(plotly,highlight)
importFrom(plotly,layout)
importFrom(plotly,orca)
importFrom(plotly,plotlyOutput)
importFrom(plotly,plotlyProxy)
importFrom(plotly,plotlyProxyInvoke)
importFrom(plotly,renderPlotly)
importFrom(plotly,subplot)
importFrom(progress,progress_bar)
importFrom(rhandsontable,hot_col)
importFrom(rhandsontable,hot_to_r)
importFrom(rhandsontable,rHandsontableOutput)
importFrom(rhandsontable,renderRHandsontable)
importFrom(rhandsontable,rhandsontable)
importFrom(rhdf5,h5createDataset)
importFrom(rhdf5,h5createFile)
importFrom(rhdf5,h5createGroup)
importFrom(rhdf5,h5delete)
importFrom(rhdf5,h5write)
importFrom(rtracklayer,TwoBitFile)
importFrom(rtracklayer,export)
importFrom(rtracklayer,import)
importFrom(rtracklayer,track)
importFrom(shinyFiles,getVolumes)
importFrom(shinyFiles,parseDirPath)
importFrom(shinyFiles,parseFilePaths)
importFrom(shinyFiles,parseSavePath)
importFrom(shinyFiles,shinyDirButton)
importFrom(shinyFiles,shinyDirChoose)
importFrom(shinyFiles,shinyFileChoose)
importFrom(shinyFiles,shinyFileSave)
importFrom(shinyFiles,shinyFilesButton)
importFrom(shinyFiles,shinySaveButton)
importFrom(shinyWidgets,actionBttn)
importFrom(shinyWidgets,ask_confirmation)
importFrom(shinyWidgets,radioGroupButtons)
importFrom(shinyWidgets,sendSweetAlert)
importFrom(shinyWidgets,sliderTextInput)
importFrom(shinyWidgets,switchInput)
importFrom(shinyWidgets,updateRadioGroupButtons)
importFrom(shinyWidgets,updateSliderTextInput)
importFrom(stats,aggregate)
importFrom(stats,as.formula)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,prcomp)
importFrom(stats,qt)
importFrom(stats,runif)
importFrom(tools,R_user_dir)
importFrom(utils,download.file)
importFrom(utils,getFromNamespace)
importFrom(utils,packageVersion)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
useDynLib(SpliceWiz, .registration = TRUE)
