# Generated by roxygen2: do not edit by hand

export("assay<-")
export("assayNames<-")
export("assays<-")
export("colData<-")
export("rowData<-")
export(BAM2COV)
export(BuildReference)
export(BuildReference_Full)
export(CollateData)
export(CoordToGR)
export(DESeq_ASE)
export(DoubleExpSeq_ASE)
export(Find_Bams)
export(Find_FASTQ)
export(Find_IRFinder_Output)
export(Find_Samples)
export(GetCoverage)
export(GetCoverageBins)
export(GetCoverageRegions)
export(GetCoverage_DF)
export(GetNonPolyARef)
export(GetReferenceResource)
export(IRFinder)
export(IsCOV)
export(MakeSE)
export(Mappability_CalculateExclusions)
export(Mappability_GenReads)
export(NxtFilter)
export(NxtIRF_example_NxtSE)
export(NxtIRF_example_bams)
export(Plot_Coverage)
export(Plot_Genome)
export(STAR_Mappability)
export(STAR_align_experiment)
export(STAR_align_fastq)
export(STAR_buildRef)
export(STAR_version)
export(apply_filters)
export(as_egg_ggplot)
export(assay)
export(assayNames)
export(assays)
export(colData)
export(get_default_filters)
export(limma_ASE)
export(make_diagonal)
export(make_matrix)
export(rowData)
export(runFilter)
export(theme_white)
export(theme_white_legend)
export(theme_white_legend_plot_track)
exportClasses(NxtFilter)
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(rbind)
exportMethods(realize_NxtSE)
exportMethods(ref)
exportMethods(sampleQC)
exportMethods(up_exc)
exportMethods(up_inc)
import(NxtIRFdata)
import(data.table)
import(ggplot2)
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(DelayedArray,DelayedArray)
importFrom(DelayedArray,plogis)
importFrom(DelayedArray,qlogis)
importFrom(DelayedArray,rowMeans)
importFrom(DelayedArray,rowSums)
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(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,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(fst,read.fst)
importFrom(fst,write.fst)
importFrom(genefilter,rowttests)
importFrom(magrittr,"%>%")
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,coerce)
importFrom(methods,is)
importFrom(methods,new)
importFrom(parallel,detectCores)
importFrom(plotly,config)
importFrom(plotly,event_data)
importFrom(plotly,ggplotly)
importFrom(plotly,highlight)
importFrom(plotly,layout)
importFrom(plotly,plotlyOutput)
importFrom(plotly,plotlyProxy)
importFrom(plotly,plotlyProxyInvoke)
importFrom(plotly,renderPlotly)
importFrom(plotly,subplot)
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(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(NxtIRFcore, .registration = TRUE)
