├── .gitignore ├── .travis.yml ├── CHANGES ├── LICENSE.TXT ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile ├── bam.rst ├── biascorrecting.rst ├── conf.py ├── faqs.rst ├── footprinting.rst ├── images │ ├── FMR1a.png │ ├── FMR1b.png │ ├── K562AP1ChIP.png │ ├── K562CTCFChIP.png │ ├── eboxbias.png │ └── example_footprint_scores_output.png ├── index.rst ├── installation.rst ├── intervals.rst ├── scripts.rst └── tutorial.rst ├── examples ├── example.bam ├── example.bam.bai ├── example.bed └── footprinttest.py ├── pyDNase ├── __init__.py ├── _version.py ├── data │ ├── IMR90_6mer.pickle │ ├── example.bam │ ├── example.bam.bai │ └── example.bed ├── footprinting │ ├── WellingtonC.c │ ├── WellingtonC.h │ ├── WellingtonC.pyx │ └── __init__.py └── scripts │ ├── dnase_average_profile.py │ ├── dnase_bias_estimator.py │ ├── dnase_cut_counter.py │ ├── dnase_ddhs_scorer.py │ ├── dnase_fos_scorer.py │ ├── dnase_pretty_picture.py │ ├── dnase_to_JSON.py │ ├── dnase_to_javatreeview.py │ ├── dnase_wig_tracks.py │ ├── examples │ └── example_footprint_scores.py │ ├── wellington_bootstrap.py │ └── wellington_footprints.py ├── setup.cfg ├── setup.py └── test └── __init__.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jpiper/pyDNase/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jpiper/pyDNase/HEAD/.travis.yml -------------------------------------------------------------------------------- /CHANGES: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jpiper/pyDNase/HEAD/CHANGES -------------------------------------------------------------------------------- /LICENSE.TXT: -------------------------------------------------------------------------------- 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