NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%>%")
export(CGi)
export(CpGs)
export(DM.R)
export(DMReport)
export(DMRichCpG)
export(DMRichGenic)
export(DMRichPlot)
export(DMparseR)
export(GOfuncR)
export(GOplot)
export(HOMER)
export(Manhattan)
export(PCA)
export(annotateRegions)
export(annotationDatabases)
export(arrayLift)
export(chromHMM)
export(chromHMM_heatmap)
export(densityPlot)
export(dmrList)
export(extend)
export(getBackground)
export(getCpGs)
export(getExons)
export(gg_color_hue)
export(globalStats)
export(gr2bed)
export(imprintOverlap)
export(methylLearn)
export(plotDMRs2)
export(prepareHOMER)
export(processBismark)
export(read_excel_all)
export(roadmap)
export(roadmap_heatmap)
export(slimGO)
export(smooth2txt)
export(smoothPheatmap)
export(windows)
import(AnnotationHub)
import(BiocManager)
import(GOfuncR)
import(GenomicRanges)
import(bsseq)
import(dmrseq)
import(ensembldb, except = c(select, filter))
import(ggplot2)
import(gt)
importClassesFrom(bsseq,BSseq)
importFrom(AnnotationHub,AnnotationHub)
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,unlist)
importFrom(BiocParallel,MulticoreParam)
importFrom(Boruta,Boruta)
importFrom(Boruta,attStats)
importFrom(CMplot,CMplot)
importFrom(ChIPseeker,annotatePeak)
importFrom(DelayedMatrixStats,colMeans2)
importFrom(DelayedMatrixStats,colSums2)
importFrom(DelayedMatrixStats,rowSums2)
importFrom(GenomeInfoDb,as.data.frame)
importFrom(GenomeInfoDb,dropSeqlevels)
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,gaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,setdiff)
importFrom(GenomicRanges,sort)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,trim)
importFrom(Glimma,glMDSPlot)
importFrom(Hmisc,capitalize)
importFrom(IRanges,IRanges)
importFrom(LOLA,loadRegionDB)
importFrom(LOLA,runLOLA)
importFrom(LOLA,writeCombinedEnrichment)
importFrom(PCAtools,biplot)
importFrom(PCAtools,pca)
importFrom(PerformanceAnalytics,tol21rainbow)
importFrom(R2HTML,HTML)
importFrom(R2HTML,HTMLEndFile)
importFrom(R2HTML,HTMLInitFile)
importFrom(RColorBrewer,brewer.pal)
importFrom(broom,tidy)
importFrom(bsseq,getCoverage)
importFrom(bsseq,getMeth)
importFrom(bsseq,read.bismark)
importFrom(data.table,rbindlist)
importFrom(dmrseq,dmrseq)
importFrom(dmrseq,getAnnot)
importFrom(dmrseq,plotDMRs)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,case_when)
importFrom(dplyr,contains)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_if)
importFrom(dplyr,pull)
importFrom(dplyr,recode_factor)
importFrom(dplyr,rename)
importFrom(dplyr,rename_with)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,slice)
importFrom(dplyr,summarize)
importFrom(dplyr,tally)
importFrom(dplyr,transmute)
importFrom(dplyr,ungroup)
importFrom(enrichR,enrichr)
importFrom(enrichR,listEnrichrDbs)
importFrom(enrichR,setEnrichrSite)
importFrom(forcats,as_factor)
importFrom(forcats,fct_rev)
importFrom(ggplot2,ggsave)
importFrom(ggsci,scale_fill_d3)
importFrom(glue,glue)
importFrom(glue,glue_collapse)
importFrom(gplots,heatmap.2)
importFrom(grDevices,dev.off)
importFrom(grDevices,hcl)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,arrows)
importFrom(gt,as_raw_html)
importFrom(gt,fmt_number)
importFrom(gt,fmt_percent)
importFrom(gt,fmt_scientific)
importFrom(gt,gt)
importFrom(gt,tab_header)
importFrom(hablar,s)
importFrom(magrittr,"%>%")
importFrom(magrittr,"%T>%")
importFrom(magrittr,set_colnames)
importFrom(minfi,getAnnotation)
importFrom(openxlsx,read.xlsx)
importFrom(openxlsx,write.xlsx)
importFrom(parallel,mclapply)
importFrom(pheatmap,pheatmap)
importFrom(plyranges,as_granges)
importFrom(plyranges,count_overlaps)
importFrom(plyranges,filter)
importFrom(plyranges,join_overlap_left)
importFrom(plyranges,mutate)
importFrom(plyranges,select)
importFrom(plyranges,stretch)
importFrom(purrr,flatten)
importFrom(purrr,map)
importFrom(purrr,map_dfr)
importFrom(purrr,pluck)
importFrom(purrr,set_names)
importFrom(purrr,walk)
importFrom(rGREAT,getEnrichmentTables)
importFrom(rGREAT,plotRegionGeneAssociationGraphs)
importFrom(rGREAT,submitGreatJob)
importFrom(readxl,excel_sheets)
importFrom(readxl,read_excel)
importFrom(readxl,read_xlsx)
importFrom(rlang,sym)
importFrom(rrvgo,calculateSimMatrix)
importFrom(rrvgo,reduceSimMatrix)
importFrom(rrvgo,scatterPlot)
importFrom(rrvgo,treemapPlot)
importFrom(rtracklayer,liftOver)
importFrom(sigFeature,sigFeature)
importFrom(stats,aov)
importFrom(stats,as.formula)
importFrom(stats,fisher.test)
importFrom(stats,kmeans)
importFrom(stats,p.adjust)
importFrom(stringr,str_detect)
importFrom(stringr,str_remove)
importFrom(stringr,str_replace)
importFrom(stringr,str_to_title)
importFrom(stringr,str_trim)
importFrom(stringr,str_trunc)
importFrom(tibble,add_column)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,gather)
importFrom(tidyr,nest)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(tidyr,separate)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tidyselect,any_of)
importFrom(utils,capture.output)
importFrom(utils,installed.packages)
importFrom(utils,sessionInfo)
importFrom(utils,write.table)
importFrom(viridis,viridis)
importFrom(wesanderson,wes_palette)
importMethodsFrom(bsseq,pData)
importMethodsFrom(bsseq,sampleNames)
importMethodsFrom(bsseq,seqnames)