Pan-ChIP-seq Analysis of Peak Sets
Project description
PanChIP
Pan-ChIP-seq Analysis of Protein Colocalization Using Peak Sets
Installation
pip3 install panchip
Usage
panchip <command> [options]
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
Initialization of the PanChIP library positional arguments: library_directory Directory wherein PanChIP library will be stored. > 13.6 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
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
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)
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PanChIP-3.0.9.tar.gz
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