├── .claude └── settings.local.json ├── .github └── workflows │ ├── codeql-analysis.yml │ ├── docker-publish.yml │ ├── docs.yml │ ├── python-package-conda.yml │ ├── python-publish.yml │ └── triger-binder-build.yml ├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── coolbox ├── __init__.py ├── __main__.py ├── api.py ├── cli.py ├── core │ ├── __init__.py │ ├── browser │ │ ├── __init__.py │ │ ├── base.py │ │ └── widgets │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── full.py │ │ │ ├── navigation.py │ │ │ └── simple.py │ ├── coverage │ │ ├── __init__.py │ │ ├── base.py │ │ ├── highlights.py │ │ ├── hlines.py │ │ └── vlines.py │ ├── feature.py │ ├── frame │ │ ├── __init__.py │ │ ├── base.py │ │ ├── frame.py │ │ └── superframe │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ └── jointview.py │ └── track │ │ ├── __init__.py │ │ ├── arcs │ │ ├── __init__.py │ │ ├── base.py │ │ ├── bedpe.py │ │ ├── hicpeaks.py │ │ ├── pairs.py │ │ └── plot.py │ │ ├── bam.py │ │ ├── base.py │ │ ├── bed │ │ ├── __init__.py │ │ ├── base.py │ │ ├── bed.py │ │ └── plot.py │ │ ├── gtf.py │ │ ├── hicmat │ │ ├── __init__.py │ │ ├── base.py │ │ ├── cool.py │ │ ├── dothic.py │ │ ├── hicdiff │ │ │ ├── __init__.py │ │ │ ├── diff.py │ │ │ └── selfish.py │ │ ├── hicmat.py │ │ ├── plot.py │ │ └── process.py │ │ ├── hist │ │ ├── __init__.py │ │ ├── bam.py │ │ ├── base.py │ │ ├── bedgraph.py │ │ ├── bigwig.py │ │ ├── hicfeature.py │ │ ├── plot.py │ │ └── snp.py │ │ ├── ideogram.py │ │ ├── pseudo.py │ │ └── tad.py ├── genome │ ├── hg19.txt │ ├── hg38.txt │ ├── mm10.txt │ └── mm9.txt └── utilities │ ├── __init__.py │ ├── cmd.py │ ├── doctool.py │ ├── figtools.py │ ├── filetool.py │ ├── fmtconvert.py │ ├── genome.py │ ├── logtools.py │ └── reader │ ├── __init__.py │ ├── hic │ ├── __init__.py │ ├── straw.py │ ├── tools.py │ └── wrap.py │ └── tab.py ├── docker ├── Dockerfile └── readme.md ├── docs ├── .nojekyll ├── Makefile ├── images │ ├── api_and_cli.png │ ├── banner.png │ ├── browser_compose_0.png │ ├── browser_compose_1.png │ ├── browser_compose_2.png │ ├── browser_show_0.png │ ├── fig_CLI.png │ ├── title-1.png │ ├── title-2.png │ └── title.png ├── source │ ├── _gallery │ │ ├── HiCDiff.ipynb │ │ ├── TADs.ipynb │ │ ├── arcs_cov.ipynb │ │ ├── arcs_style.ipynb │ │ ├── bed_chr9_4000000_6000000.bed.bgz │ │ ├── bed_chr9_4000000_6000000.bed.bgz.tbi │ │ ├── bw_cov.ipynb │ │ ├── decay.ipynb │ │ ├── dna_features.ipynb │ │ ├── hicfeature.ipynb │ │ ├── hicmat_cmaps.ipynb │ │ ├── hist_style.ipynb │ │ ├── ideogram.ipynb │ │ ├── joint_view.ipynb │ │ ├── peakcov.ipynb │ │ ├── reso_normalize.ipynb │ │ ├── selfish.ipynb │ │ ├── smoothing.ipynb │ │ └── snp.ipynb │ ├── _static │ │ ├── peakachu_track.py │ │ └── pokemons │ │ │ ├── Bulbasaur.png │ │ │ ├── Charmander.png │ │ │ ├── Pikachu.png │ │ │ ├── PokeBall.png │ │ │ ├── Squirtle.png │ │ │ └── list.txt │ ├── api.rst │ ├── conf.py │ ├── custom_elements.ipynb │ ├── gallery.rst │ ├── index.rst │ ├── installation.md │ ├── quick_start_API.ipynb │ └── quick_start_CLI.ipynb └── update_notebooks.py ├── environment.yml ├── pyproject.toml ├── requirements.txt └── tests ├── TestRegion.ipynb ├── conftest.py ├── custom_track.py ├── test_add_rule.py ├── test_browser.py ├── test_cli.py ├── test_coverage.py ├── test_data ├── bam_chr9_4000000_6000000.bam ├── bed6_chr9_4000000_6000000.bed ├── bed9_chr9_4000000_6000000.bed ├── bed_chr9_4000000_6000000.bed ├── bed_chr9_4000000_6000000_chromstates.bed ├── bedgraph_chr9_4000000_6000000.bg ├── bedpe_chr9_4000000_6000000.bedpe ├── bedpe_var_chr9_4000000_6000000.bedpe ├── bigwig_chr9_4000000_6000000.bw ├── bigwig_chr9_4000000_6000000_K562_H3K27ac.bigwig ├── bigwig_chr9_4000000_6000000_K562_H3K27me3.bigwig ├── bigwig_chr9_4000000_6000000_K562_H3K4me3.bigwig ├── bigwig_chr9_4000000_6000000_K562_RNA.bigwig ├── chr9.1.pc.bedGraph ├── cool_chr1_89000000_90400000_for_cmp_1.mcool ├── cool_chr1_89000000_90400000_for_cmp_2.mcool ├── cool_chr9_4000000_6000000.mcool ├── 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