Pan-ChIP-seq Analysis of Peak Sets
Project description
PanChIP
Pan-ChIP-seq Analysis of Protein Colocalization Using Peak Sets
Installation
pip install panchip
Usage
panchip [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. > 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
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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