├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── DevelopperGuide ├── DevelopperGuide.Rmd └── DevelopperGuide.html ├── Makefile ├── NAMESPACE ├── R ├── bed_import.R ├── bed_to_granges.R ├── compute_enrichment.R ├── count_mapped_peaks.R ├── data.R ├── download_encode_peaks.R ├── download_remap_catalog.R ├── download_ucsc_chrom_sizes.R ├── enrichment.R ├── enrichment_bar_plot.R ├── enrichment_dot_plot.R ├── enrichment_volcano_plot.R ├── export_enrichment.R ├── extract_enrichment.R ├── fit_poisson.R ├── gen_regions.R ├── granges_to_bed.R ├── import_chrom_sizes.R ├── intersect.R ├── load_chrom_file.R ├── load_chrom_sizes.R ├── loladb_to_catalog.R ├── random_intersections.R ├── roken.R ├── shuffle.R └── text_outline.R ├── README.md ├── ReMapEnrich.Rproj ├── _config.yml ├── data ├── enrichment_example.RData └── random_regions_vs_ReMap.RData ├── graph ├── Histograms │ ├── AFF4.pdf │ ├── AHR.pdf │ ├── AR.pdf │ ├── ARID3A.pdf │ ├── ARNT.pdf │ ├── ATF1.pdf │ ├── ATF2.pdf │ ├── ATF3.pdf │ ├── ATRX.pdf │ ├── BACH1.pdf │ ├── BATF.pdf │ ├── BCL11A.pdf │ ├── BCL3.pdf │ ├── BCL6.pdf │ ├── BCLAF1.pdf │ ├── BCOR.pdf │ ├── BDP1.pdf │ ├── BHLHE40.pdf │ ├── BRCA1.pdf │ ├── BRD2.pdf │ ├── BRD3.pdf │ ├── BRD4.pdf │ ├── BRF1.pdf │ ├── BRF2.pdf │ ├── CBFB.pdf │ ├── CBX3.pdf │ ├── CCNT2.pdf │ ├── CDK8.pdf │ ├── CDK9.pdf │ ├── CDX2.pdf │ ├── CEBPA.pdf │ ├── CEBPB.pdf │ ├── CEBPD.pdf │ ├── CHD1.pdf │ ├── CHD2.pdf │ ├── CREB1.pdf │ ├── CTBP2.pdf │ ├── CTCF.pdf │ ├── CTCFL.pdf │ ├── CTNNB1.pdf │ ├── DCP1A.pdf │ ├── E2F1.pdf │ ├── E2F4.pdf │ ├── E2F6.pdf │ ├── E2F7.pdf │ ├── EBF1.pdf │ ├── EGR1.pdf │ ├── ELF1.pdf │ ├── ELF5.pdf │ ├── ELK1.pdf │ ├── ELK4.pdf │ ├── ELL2.pdf │ ├── EOMES.pdf │ ├── ERG.pdf │ ├── ESR1.pdf │ ├── ESR2.pdf │ ├── ESRRA.pdf │ ├── ETS1.pdf │ ├── ETV1.pdf │ ├── EZH2.pdf │ ├── FAM48A.pdf │ ├── FLI1.pdf │ ├── FOS.pdf │ ├── FOSL1.pdf │ ├── FOSL2.pdf │ ├── FOXA1.pdf │ ├── FOXA2.pdf │ ├── FOXH1.pdf │ ├── FOXM1.pdf │ ├── FOXP1.pdf │ ├── FOXP2.pdf │ ├── GABPA.pdf │ ├── GATA1.pdf │ ├── GATA2.pdf │ ├── GATA3.pdf │ ├── GATA6.pdf │ ├── GATAD1.pdf │ ├── GPS2.pdf │ ├── GREB1.pdf │ ├── GTF2B.pdf │ ├── GTF2F1.pdf │ ├── GTF3C2.pdf │ ├── HDAC1.pdf │ ├── HDAC2.pdf │ ├── HDAC6.pdf │ ├── HDAC8.pdf │ ├── HMGN3.pdf │ ├── HNF4A.pdf │ ├── HNF4G.pdf │ ├── HSF1.pdf │ ├── IKZF1.pdf │ ├── IRF1.pdf │ ├── IRF3.pdf │ ├── IRF4.pdf │ ├── JUN.pdf │ ├── JUNB.pdf │ ├── JUND.pdf │ ├── KDM5A.pdf │ ├── KDM5B.pdf │ ├── KLF4.pdf │ ├── MAFF.pdf │ ├── MAFK.pdf │ ├── MAX.pdf │ ├── MAZ.pdf │ ├── MBD4.pdf │ ├── MED12.pdf │ ├── MEF2A.pdf │ ├── MEF2C.pdf │ ├── MEIS1.pdf │ ├── MTA3.pdf │ ├── MXI1.pdf │ ├── MYBL2.pdf │ ├── MYC.pdf │ ├── NANOG.pdf │ ├── NCOA1.pdf │ ├── NCOR1.pdf │ ├── NCOR2.pdf │ ├── NELFE.pdf │ ├── NF1C.pdf │ ├── NFATC1.pdf │ ├── NFE2.pdf │ ├── NFKB1.pdf │ ├── NFYA.pdf │ ├── NFYB.pdf │ ├── NIPBL.pdf │ ├── NKX2-1.pdf │ ├── NKX3-1.pdf │ ├── NOTCH1.pdf │ ├── NR2C2.pdf │ ├── NR2F2.pdf │ ├── NR3C1.pdf │ ├── NR3C3.pdf │ ├── NRF1.pdf │ ├── ONECUT1.pdf │ ├── ORC1.pdf │ ├── PAX5.pdf │ ├── PBX3.pdf │ ├── PHF8.pdf │ ├── PML.pdf │ ├── POU2F2.pdf │ ├── POU5F1.pdf │ ├── PPARG.pdf │ ├── PPARGC1A.pdf │ ├── PRAME.pdf │ ├── PRDM1.pdf │ ├── PRDM14.pdf │ ├── RAC3.pdf │ ├── RAD21.pdf │ ├── RB1.pdf │ ├── RBBP5.pdf │ ├── RBPJ.pdf │ ├── RCOR1.pdf │ ├── RELA.pdf │ ├── REST.pdf │ ├── RFX5.pdf │ ├── RNF2.pdf │ ├── RPC155.pdf │ ├── RUNX1+3.pdf │ ├── RUNX1.pdf │ ├── RUNX1T1.pdf │ ├── RUNX2.pdf │ ├── RUNX3.pdf │ ├── RXRA.pdf │ ├── SAP30.pdf │ ├── SETDB1.pdf │ ├── SFMBT1.pdf │ ├── SIN3A.pdf │ ├── SIRT6.pdf │ ├── SIX5.pdf │ ├── SMAD1.pdf │ ├── SMAD2+3.pdf │ ├── SMAD3.pdf │ ├── SMAD4.pdf │ ├── SMARCA4.pdf │ ├── SMARCB1.pdf │ ├── SMARCC1.pdf │ ├── SMARCC2.pdf │ ├── SMC1A.pdf │ ├── SMC3.pdf │ ├── SMC4.pdf │ ├── SNAPC1.pdf │ ├── SNAPC4.pdf │ ├── SNAPC5.pdf │ ├── SOX2.pdf │ ├── SP1.pdf │ ├── SP2.pdf │ ├── SP4.pdf │ ├── SPI1.pdf │ ├── SREBP1.pdf │ ├── SRF.pdf │ ├── STAG1.pdf │ ├── STAT1.pdf │ ├── STAT2.pdf │ ├── STAT3.pdf │ ├── STAT4.pdf │ ├── STAT5A.pdf │ ├── STAT5B.pdf │ ├── SUZ12.pdf │ ├── TAF1.pdf │ ├── TAF2.pdf │ ├── TAF3.pdf │ ├── TAF7.pdf │ ├── TAL1.pdf │ ├── TAp73a.pdf │ ├── TAp73b.pdf │ ├── TBL1.pdf │ ├── TBL1XR1.pdf │ ├── TBP.pdf │ ├── TCF12.pdf │ ├── TCF3.pdf │ ├── TCF4.pdf │ ├── TCF7L2.pdf │ ├── TEAD4.pdf │ ├── TFAP2A.pdf │ ├── TFAP2C.pdf │ ├── TFAP4.pdf │ ├── THAP1.pdf │ ├── TLE3.pdf │ ├── TP53.pdf │ ├── TP63.pdf │ ├── TRIM28.pdf │ ├── UBTF.pdf │ ├── USF1.pdf │ ├── USF2.pdf │ ├── VDR.pdf │ ├── WRNIP1.pdf │ ├── YY1.pdf │ ├── ZBTB33.pdf │ ├── ZBTB7A.pdf │ ├── ZEB1.pdf │ ├── ZKSCAN1.pdf │ ├── ZNF143.pdf │ ├── ZNF217.pdf │ ├── ZNF263.pdf │ ├── ZNF274.pdf │ ├── ZNF76.pdf │ └── ZZZ3.pdf └── VarVSMean.pdf ├── inst └── extdata │ ├── ReMap_nrPeaks_public_chr22.bed │ ├── ReMap_nrPeaks_public_chr22_SOX2.bed │ ├── hg19.genome │ ├── hg38.genome │ └── tair10.genome ├── man ├── ReMapEnrich.Rd ├── bedImport.Rd ├── bedToGranges.Rd ├── computeEnrichment.Rd ├── countMappedPeaks.Rd ├── downloadEncodePeaks.Rd ├── downloadRemapCatalog.Rd ├── downloadUcscChromSizes.Rd ├── enrichment.Rd ├── enrichmentBarPlot.Rd ├── enrichmentDotPlot.Rd ├── enrichmentVolcanoPlot.Rd ├── exportEnrichment.Rd ├── extractEnrichment.Rd ├── fitPoisson.Rd ├── genRegions.Rd ├── grangesToBed.Rd ├── importChromSizes.Rd ├── intersect.Rd ├── loadChromFile.Rd ├── loadChromSizes.Rd ├── lolaDBToCatalog.Rd ├── randomIntersections.Rd ├── shuffle.Rd └── textOutline.Rd ├── misc ├── de_novo_enrichment.R ├── example1.R └── install_dependencies.R └── vignettes ├── advanced_use.R ├── advanced_use.Rmd ├── advanced_use.html ├── advanced_use.md ├── basic_use.R ├── basic_use.Rmd ├── basic_use.html ├── basic_use.md ├── basic_use_files └── figure-html │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ ├── unnamed-chunk-6-1.png │ └── unnamed-chunk-7-1.png ├── bibliography.bib ├── biomed-central.csl ├── nucleic-acids-research.csl ├── statistical_validation.R ├── statistical_validation.Rmd ├── statistical_validation.html ├── statistical_validation.md └── statistical_validation_files └── 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