# Generated by roxygen2: do not edit by hand

export(SummarizedCounts)
export(calc_gene_gc)
export(calc_region_gc)
export(correct_GC)
export(correct_IR)
export(correct_global)
export(correct_stranded)
export(create_summarizedcounts)
export(get_region_stat)
export(get_saf)
export(plot_assignment_stat)
export(plot_expr_distr)
export(plot_gene_content)
export(plot_pca_heatmap)
export(plot_read_distr)
export(plot_sample_corr)
export(salmon_tximport)
export(style_BSgenome)
export(summarize_reads)
import(DESeq2)
import(ggplot2)
importFrom(AnnotationFilter,AnnotationFilter)
importFrom(AnnotationFilter,GeneBiotypeFilter)
importFrom(AnnotationFilter,SeqNameFilter)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,"width<-")
importFrom(BiocGenerics,width)
importFrom(Biostrings,letterFrequency)
importFrom(GenomeInfoDb,"seqnames<-")
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,setdiff)
importFrom(KernSmooth,bkde2D)
importFrom(R6,R6Class)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,seqinfo)
importFrom(Rsubread,featureCounts)
importFrom(SummarizedExperiment,assay)
importFrom(edgeR,cpm)
importFrom(edgeR,filterByExpr)
importFrom(ensembldb,EnsDb)
importFrom(ensembldb,exons)
importFrom(ensembldb,exonsBy)
importFrom(ensembldb,genes)
importFrom(ensembldb,seqlevels)
importFrom(ensembldb,transcripts)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,pairs)
importFrom(graphics,par)
importFrom(graphics,smoothScatter)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(limma,lmFit)
importFrom(limma,voom)
importFrom(methods,as)
importFrom(methods,is)
importFrom(pheatmap,pheatmap)
importFrom(qsmooth,qsmooth)
importFrom(qsmooth,qsmoothData)
importFrom(reshape2,melt)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(tximport,tximport)
importFrom(utils,read.delim)
importFrom(utils,write.table)
