├── README.md └── Scripts ├── Align_bash ├── align_DRIP_seq_paired.sh ├── align_single.sh ├── bam2bed.sh ├── call_macs.sh ├── dripseq_ce10.sh └── dripseq_mm9.sh ├── CpGfreq_GCcontent └── CpGfreq_GCcontent.R ├── DRIPseq_G4ChIPseqMEthylation_onHOT └── Figure4.R ├── Define_HOT_regions ├── TFsonHOT.R ├── hot_organism.R ├── peak_rank_HOT.R ├── peaker_adapted.R └── schema_figure.R ├── Expression_on_HOT ├── 20160914-public-3.0.0-FwVjFU-mm9-all-gene.txt ├── E-MTAB-3578-query-results.tsv ├── GeneExpression.R └── checkExpression.R ├── GREAT_output ├── GOterms.R ├── hg19 │ ├── HOThg19_filterNearBy2kb_Uniform_nopol2a_windows_top1perc_ucsc.bed │ ├── shown-GOBiologicalProcess.tsv │ └── shown-GOMolecularFunction.tsv └── mm9 │ ├── HOTmm9_nopol2a_windows_top1perc_ucsc.bed │ ├── shown-GOBiologicalProcess.tsv │ └── shown-GOMolecularFunction.tsv ├── Generic_ML ├── MLreport_cpgi.R ├── MLreport_cpgi_functions.R ├── MLreport_functions.R ├── generic_ML_for_kmer_hot.regions.R ├── hot_functions.R └── 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