# Generated by roxygen2: do not edit by hand

export(RNAattributes)
export(RNAdf2se)
export(RNAdicercall)
export(RNAdifferentialAnalysis)
export(RNAdistribution)
export(RNAfeatures)
export(RNAimport)
export(RNAmergeAnnotations)
export(RNAmergeGenomes)
export(RNAmobile)
export(RNApopulation)
export(RNAreorder)
export(RNAsequences)
export(RNAsubset)
export(RNAsummary)
export(mapRNA)
export(plotHeatmap)
export(plotRNAfeatures)
export(plotSampleDistance)
export(plotSamplePCA)
importFrom(BiocGenerics,grep)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,writeXStringSet)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,plotPCA)
importFrom(DESeq2,results)
importFrom(DESeq2,rlog)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,seqnames)
importFrom(IRanges,IRanges)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,ranges)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SimDesign,quiet)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(bioseq,rna)
importFrom(bioseq,seq_consensus)
importFrom(data.table,":=")
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,melt)
importFrom(data.table,setDT)
importFrom(data.table,setnames)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,case_when)
importFrom(dplyr,contains)
importFrom(dplyr,count)
importFrom(dplyr,filter)
importFrom(dplyr,if_any)
importFrom(dplyr,inner_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_at)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,starts_with)
importFrom(dplyr,where)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,exactTest)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(pheatmap,pheatmap)
importFrom(progress,progress_bar)
importFrom(reticulate,use_condaenv)
importFrom(rlang,sym)
importFrom(rtracklayer,export)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.gff)
importFrom(scales,label_percent)
importFrom(stats,complete.cases)
importFrom(stats,dist)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,relevel)
importFrom(stats,setNames)
importFrom(tidyr,gather)
importFrom(tidyr,replace_na)
importFrom(tidyselect,all_of)
importFrom(tidyselect,starts_with)
importFrom(utils,flush.console)
importFrom(utils,read.table)
importFrom(utils,write.table)
