├── .github ├── .gitignore └── workflows │ ├── check-bioc.yml │ └── pkgdown.yaml ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── excluderanges.R └── zzz.R ├── README.Rmd ├── README.md ├── inst ├── CITATION ├── extdata │ └── metadata.csv └── scripts │ ├── make-data.R │ └── make-metadata.R ├── man ├── T2T.CHM13.chm13.draft_v1.1.telomere.Rd ├── T2T.CHM13.chm13.draft_v2.0.cen_mask.Rd ├── T2T.Lareau.chm13v2.0_peaks.Rd ├── T2T.UCSC.censat.Rd ├── T2T.UCSC.gap.Rd ├── T2T.UCSC.hgUnique.hg38.Rd ├── T2T.excluderanges.Rd ├── TAIR10.Klasfeld.arabidopsis_Excludable_20inputs.Rd ├── TAIR10.Klasfeld.arabidopsis_greenscreen_20inputs.Rd ├── TAIR10.UCSC.araTha1.gap.Rd ├── TAIR10.Wimberley.predicted_excluded_list_sorted_0.6.Rd ├── ce10.Boyle.ce10-Excludable.v2.Rd ├── ce10.Kundaje.ce10-Excludable.Rd ├── ce11.Boyle.ce11-Excludable.v2.Rd ├── danRer10.Domingues.Excludableed.Rd ├── danRer10.UCSC.contig.Rd ├── danRer10.UCSC.scaffold.Rd ├── danRer10.Yang.Supplemental_Table_19.ChIP-seq_black_list_in_the_zebrafish_genome.Rd ├── dm3.Boyle.dm3-Excludable.v2.Rd ├── dm3.Kundaje.dm3-Excludable.Rd ├── dm3.UCSC.contig.Rd ├── dm3.UCSC.scaffold.Rd ├── dm6.Boyle.dm6-Excludable.v2.Rd ├── dm6.UCSC.other.Rd ├── excluderanges.Rd ├── figures │ ├── README-GenomicDistributions1-1.png │ ├── README-excluderanges_hg38_Reddy_metadata-1.png │ ├── README-excluderanges_hg38_count-1.png │ ├── README-excluderanges_hg38_jaccard-1.png │ ├── README-excluderanges_hg38_overlap_coefficient-1.png │ ├── README-excluderanges_hg38_sumwidth-1.png │ ├── README-excluderanges_hg38_width-1.png │ ├── README-gapcounts-1.png │ ├── Table_S1.csv │ ├── excluderanges_hg19_gaps_number.png │ ├── excluderanges_hg38_Reddy_metadata.png │ ├── excluderanges_hg38_count.png │ ├── excluderanges_hg38_jaccard.png │ ├── excluderanges_hg38_sumwidth.png │ ├── excluderanges_hg38_width.png │ └── logo.png ├── hg19.Bernstein.Mint_Excludable_hg19.Rd ├── hg19.Birney.wgEncodeDacMapabilityConsensusExcludable.Rd ├── hg19.Boyle.hg19-Excludable.v2.Rd ├── hg19.Crawford.wgEncodeDukeMapabilityRegionsExcludable.Rd ├── hg19.Lareau.hg19.full.Excludable.Rd ├── hg19.Lareau.hg19_peaks.Rd ├── hg19.UCSC.centromere.Rd ├── hg19.UCSC.clone.Rd ├── hg19.UCSC.contig.Rd ├── hg19.UCSC.heterochromatin.Rd ├── hg19.UCSC.numtS.Rd ├── hg19.UCSC.scaffold.Rd ├── hg19.UCSC.short_arm.Rd ├── hg19.UCSC.telomere.Rd ├── hg19.Wold.hg19mitoExcludable.Rd ├── hg19.Yeo.eCLIP_Excludableregions.hg19.Rd ├── hg38.Bernstein.Mint_Excludable_GRCh38.Rd ├── hg38.Boyle.hg38-Excludable.v2.Rd ├── hg38.Kundaje.GRCh38.Excludable.Rd ├── hg38.Kundaje.GRCh38_unified_Excludable.Rd ├── hg38.Lareau.hg38.full.Excludable.Rd ├── hg38.Lareau.hg38_peaks.Rd ├── hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38.Rd ├── hg38.UCSC.centromere.Rd ├── hg38.UCSC.contig.Rd ├── hg38.UCSC.heterochromatin.Rd ├── hg38.UCSC.scaffold.Rd ├── hg38.UCSC.short_arm.Rd ├── hg38.UCSC.telomere.Rd ├── hg38.Wimberley.peakPass60Perc_sorted.Rd ├── hg38.Wold.hg38mitoExcludable.Rd ├── hg38.Yeo.eCLIP_Excludableregions.hg38liftover.bed.fixed.Rd ├── mm10.Boyle.mm10-Excludable.v2.Rd ├── mm10.Hardison.Excludable.full.Rd ├── mm10.Hardison.psuExcludable.mm10.Rd ├── mm10.Kundaje.anshul.Excludable.mm10.Rd ├── mm10.Kundaje.mm10.Excludable.Rd ├── mm10.Lareau.mm10.full.Excludable.Rd ├── mm10.Lareau.mm10_peaks.Rd ├── mm10.UCSC.centromere.Rd ├── mm10.UCSC.clone.Rd ├── mm10.UCSC.contig.Rd ├── mm10.UCSC.fragment.Rd ├── mm10.UCSC.other.Rd ├── mm10.UCSC.scaffold.Rd ├── mm10.UCSC.short_arm.Rd ├── mm10.UCSC.telomere.Rd ├── mm10.Wold.mm10mitoExcludable.Rd ├── mm39.UCSC.centromere.Rd ├── mm39.UCSC.contig.Rd ├── mm39.UCSC.scaffold.Rd ├── mm39.UCSC.short_arm.Rd ├── mm39.UCSC.telomere.Rd ├── mm39.excluderanges.Rd ├── mm9.Lareau.mm9.full.Excludable.Rd ├── mm9.Lareau.mm9_peaks.Rd ├── mm9.UCSC.centromere.Rd ├── mm9.UCSC.contig.Rd ├── mm9.UCSC.fragment.Rd ├── mm9.UCSC.numtS.Rd └── mm9.Wold.mm9mitoExcludable.Rd └── vignettes ├── excluderanges.Rmd └── references.bib /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/workflows/check-bioc.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dozmorovlab/excluderanges/HEAD/.github/workflows/check-bioc.yml -------------------------------------------------------------------------------- /.github/workflows/pkgdown.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dozmorovlab/excluderanges/HEAD/.github/workflows/pkgdown.yaml -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 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