Metadata-Version: 2.1
Name: PanChIP
Version: 3.0.0
Summary: Pan-ChIP-seq Analysis of Peak Sets
Home-page: https://github.com/hanjunlee21/PanChIP
Author: Hanjun Lee
Author-email: hanjun@mit.edu
License: MIT
Download-URL: https://github.com/hanjunlee21/PanChIP/archive/refs/tags/v.3.0.0.tar.gz
Description: # PanChIP
        
        [![PyPI version](https://badge.fury.io/py/PanChIP.svg)](https://badge.fury.io/py/PanChIP)
        
        **Pan-ChIP-seq Analysis of Protein Colocalization Using Peak Sets**
        
        ## Installation
        ```shell
        pip install panchip
        ```
        
        ## Usage
        
        ### panchip <command> [options]
        
        ```shell
        Commands:
            init            Initialization of the PanChIP library
            analysis        Analysis of a list peak sets
            filter          Filtering library for quality control
        Run panchip <command> -h for help on a specific command.
        
        PanChIP: Pan-ChIP-seq Analysis of Peak Sets
        
        positional arguments:
          command     Subcommand to run
        
        optional arguments:
          -h, --help  show this help message and exit
          --version   show program's version number and exit
        ```
        
        ### panchip init [-h] library_directory
        
        ```shell
        
        Initialization of the PanChIP library
        
        positional arguments:
          library_directory  Directory wherein PanChIP library will be stored. > 4.2
                             GB of storage required.
        
        optional arguments:
          -h, --help         show this help message and exit
        ```
        
        ### panchip analysis [-h] [-t THREADS] [-r REPEATS] library_directory input_directory output_directory
        
        ```shell
        
        Analysis of a list peak sets
        
        positional arguments:
          library_directory  Directory wherein PanChIP library was stored.
          input_directory    Input directory wherein peak sets in the format of .bed
                             files are located.
                             (.bed6 format with numeric scores in 5th column required)
          output_directory   Output directory wherein output files will be stored.
        
        optional arguments:
          -h, --help         show this help message and exit
          -t THREADS         Number of threads to use. (default: 1)
          -r REPEATS         Number of repeats to perform. (default: 1)
        ```
        
        ### panchip filter [-h] [-t THREADS] library_directory input_file output_directory
        
        ```shell
        
        Filtering library for quality control
        
        positional arguments:
          library_directory  Directory wherein PanChIP library was stored.
          input_file         Path to the input .bed file.
                             (.bed6 format with numeric scores in 5th column required)
          output_directory   Output directory wherein output files will be stored.
        
        optional arguments:
          -h, --help         show this help message and exit
          -t THREADS         Number of threads to use. (default: 1)
        ```
        
Keywords: chip-seq,bedfile
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.0
Classifier: Programming Language :: Python :: 3.1
Classifier: Programming Language :: Python :: 3.2
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Awk
Classifier: Programming Language :: Unix Shell
Description-Content-Type: text/markdown
