├── .gitignore ├── ChangeLog ├── LICENSE ├── MANIFEST ├── MANIFEST.in ├── PePr.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── entry_points.txt ├── requires.txt └── top_level.txt ├── PePr ├── PePr.py ├── __init__.py ├── classDef.py ├── data │ ├── NA__PePr_parameters.txt │ ├── NA__PePr_peaks.bed │ ├── chip_rep1.bed │ ├── chip_rep2.bed │ ├── example_command │ ├── example_parameter_file.txt │ ├── input_rep1.bed │ ├── input_rep2.bed │ ├── test__PePr_parameters.txt │ └── test__PePr_peaks.bed ├── logConfig.py ├── misc.py ├── optParser.py ├── post_processing │ ├── __init__.py │ └── post_process_PePr.py ├── pre_processing │ ├── __init__.py │ ├── cal_normalization.py │ ├── estimate_shiftSize.py │ ├── fileParser.py │ ├── initialize.py │ ├── preProcess.py │ ├── shiftSize.py │ └── windowSize.py ├── prepareData.py ├── sigTests.py └── utilities │ ├── __init__.py │ ├── cal_duplication_rate.py │ ├── cal_max_duplicates_to_keep.py │ └── find_peak_mode.py ├── README.md ├── README.pdf ├── dist ├── PePr-1.0.1.tar.gz ├── PePr-1.0.2.tar.gz ├── PePr-1.0.2a.tar.gz ├── PePr-1.0.3.tar.gz ├── PePr-1.0.3a.tar.gz ├── PePr-1.0.3b.tar.gz ├── PePr-1.0.4.tar.gz ├── PePr-1.0.5.tar.gz ├── PePr-1.0.6.tar.gz ├── PePr-1.0.7.tar.gz ├── PePr-1.0.8.tar.gz ├── PePr-1.0.9.tar.gz ├── PePr-1.0.9beta.tar.gz ├── PePr-1.1.0.tar.gz ├── PePr-1.1.1.tar.gz ├── PePr-1.1.10.tar.gz ├── PePr-1.1.11.tar.gz ├── PePr-1.1.12.tar.gz ├── PePr-1.1.13.tar.gz ├── PePr-1.1.14.tar.gz ├── PePr-1.1.15.tar.gz ├── PePr-1.1.16.tar.gz ├── PePr-1.1.17.tar.gz ├── PePr-1.1.18.tar.gz ├── PePr-1.1.19.tar.gz ├── PePr-1.1.2.tar.gz ├── PePr-1.1.20.tar.gz ├── PePr-1.1.21.tar.gz ├── PePr-1.1.22.tar.gz ├── PePr-1.1.23.tar.gz ├── PePr-1.1.24.tar.gz ├── PePr-1.1.3.tar.gz ├── PePr-1.1.4.tar.gz ├── PePr-1.1.5.tar.gz ├── PePr-1.1.6.tar.gz ├── PePr-1.1.7.tar.gz ├── PePr-1.1.8.tar.gz └── PePr-1.1.9.tar.gz ├── setup.py ├── setup.py.new └── setup.py.patch /.gitignore: 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