├── .gitignore ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── bin ├── nucleoatac └── pyatac ├── docs ├── faq.md ├── index.md ├── installation.md ├── nucleoatac.md └── pyatac.md ├── example ├── README.txt ├── example.Scores.bedgraph.gz ├── example.Scores.bedgraph.gz.tbi ├── example.VMat ├── example.bam ├── example.bam.bai ├── example.bed ├── example.slopped.bed ├── example_results │ ├── example.VMat │ ├── example.VMat.eps │ ├── example.fragmentsizes.txt │ ├── example.ins.bedgraph.gz │ ├── example.ins.bedgraph.gz.tbi │ ├── example.nfrpos.bed.gz │ ├── example.nfrpos.bed.gz.tbi │ ├── example.nuc_dist.eps │ ├── example.nuc_dist.txt │ ├── example.nucleoatac_signal.bedgraph.gz │ ├── example.nucleoatac_signal.bedgraph.gz.tbi │ ├── example.nucleoatac_signal.smooth.bedgraph.gz │ ├── example.nucleoatac_signal.smooth.bedgraph.gz.tbi │ ├── example.nucmap_combined.bed.gz │ ├── example.nucmap_combined.bed.gz.tbi │ ├── example.nucpos.bed.gz │ ├── example.nucpos.bed.gz.tbi │ ├── example.nucpos.redundant.bed.gz │ ├── example.nucpos.redundant.bed.gz.tbi │ ├── example.occ.bedgraph.gz │ ├── example.occ.bedgraph.gz.tbi │ ├── example.occ.lower_bound.bedgraph.gz │ ├── example.occ.lower_bound.bedgraph.gz.tbi │ ├── example.occ.upper_bound.bedgraph.gz │ ├── example.occ.upper_bound.bedgraph.gz.tbi │ ├── example.occ_fit.eps │ ├── example.occ_fit.txt │ ├── example.occpeaks.bed.gz │ └── example.occpeaks.bed.gz.tbi ├── sacCer3.fa ├── sacCer3.fa.fai ├── single_read.bam ├── single_read.bam.bai └── test_results │ └── README.txt ├── mkdocs.yml ├── nucleoatac ├── Magic.py ├── NFRCalling.py ├── NucleosomeCalling.py ├── Occupancy.py ├── __init__.py ├── cli.py ├── diff_occ.py ├── merge.py ├── multinomial_cov.pyx ├── run_nfr.py ├── run_nuc.py ├── run_occ.py ├── run_vprocess.py └── vplot │ ├── __init__.py │ └── standard_vplot.VMat ├── pyatac ├── Magic.py ├── VMat.py ├── __init__.py ├── bedgraph.py ├── bias.py ├── chunk.py ├── chunkmat2d.py ├── cli.py ├── fragments.pyx ├── 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