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        "author": "Rhys Newell, Mikael Boden, Alex Essebier",
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            "Development Status :: 5 - Production/Stable",
            "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "ChIP-R (\"chipper\")\n==================\n\nChIP-R uses an adaptation of the rank product statistic to assess the reproducibility of ChIP-seq peaks by incorporating information from multiple ChIP-seq replicates and \"fragmenting\" peak locations to better combine the information present across the replicates.\n\nInstall\n-------\n\n- [Python3.x](https://www.python.org/getit/) with the following packages:\n- Numpy\n- Scipy\n- pyBigWig\n\nTo install ChIP-R:\n\n    pip install ChIP-R\n\nOR if you want to install from source:\n\n    git clone https://github.com/rhysnewell/ChIP-R.git\n    cd ChIP-R\n    python3 setup.py install\n\n\n\nUsage\n-----\n\nIn the command line, type in **'chipr -h '** for detailed usage.\n\n    $ chipr -h\n\n    usage: chipr [-h] -i INPUT [INPUT ...] [-o OUTPUT] [-m MINENTRIES]\n             [--rankmethod RANKMETHOD] [--duphandling DUPHANDLING]\n             [--seed RANDOM_SEED] [-a ALPHA]\n\n    Combine multiple ChIP-seq files and return a union of all peak locations and a\n    set confident, reproducible peaks as determined by rank product analysis\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      -i INPUT [INPUT ...], --input INPUT [INPUT ...]\n                            ChIP-seq input files. These files must be in either\n                            narrowPeak, broadPeak, or regionPeak format. Multiple\n                            inputs are separeted by a single space\n      -o OUTPUT, --output OUTPUT\n                            ChIP-seq output filename prefix\n      -B, --bigbed          Specify if input files are in BigBed format\n      -m MINENTRIES, --minentries MINENTRIES\n                            The minimum peaks between replicates required to form\n                            an intersection of the peaks Default: 1\n      --rankmethod RANKMETHOD\n                            The ranking method used to rank peaks within\n                            replicates. Options: 'signalvalue', 'pvalue',\n                            'qvalue'. Default: pvalue\n      --duphandling DUPHANDLING\n                            Specifies how to handle entries that are ranked\n                            equally within a replicate Can either take the\n                            'average' ranks or a 'random' rearrangement of the\n                            ordinal ranks Options: 'average', 'random' Default:\n                            'average'\n      --seed RANDOM_SEED    Specify a seed to be used in conjunction with the\n                            'random' option for -duphandling Must be between 0 and\n                            1 Default: 0.5\n      -a ALPHA, --alpha ALPHA\n                            Alpha specifies the user cut-off value for set of\n                            reproducible peaks The analysis will still produce\n                            results including peaks within the threshold\n                            calculatedusing the binomial method Default: 0.05\n\n\n\nExample\n------\n    $ chipr -i input_prefix1.bed input_prefix2.bed input_prefix3.bed input_prefix4.bed -m 2 -o output_prefix   \n\nOutput\n------\n\nImportant result files:\n\n- **prefixname_ALL.bed**: All intersected peaks, ordered from most significant to least (10 columns)\n- **prefixname_T2.bed**: The tier 2 intersected peaks, the peaks that fall within the binomial threshold (10 columns)\n- **prefixname_T1.bed**: The tier 1 intersected peaks, the peaks that fall within the user defined threshold (10 columns)\n- **prefixname_log.txt**: A log containing the number of peaks appearing in each tier.\n\n\nprefixname.bed file has 10 columns. The output follows the standard peak format for bed files, with the addition of a 10th column that specifies the ranks of the peaks that produced this possible peak. See the toy example below.\n\n|chr |start|end  |name |score |strand  |signalValue |p-value |q-value|\n|----|-----|-----|----|------|-----|------|------|------|\n|chr1|9118 |10409|T3_peak_87823|\t491|\t.\t|15.000000\t| 0.113938|0.712353\t|\n\n\nCitation\n--------\n\n\n\n\nContact\n-------\n\nAuthors: Rhys Newell, Michael Piper, Mikael Boden, Alexandra Essebier\n\nContact:  rhys.newell(AT)uq.edu.au\n\n\n",
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