Usage

Command-line Interface

Reference Point Analysis

Analyze peaks around a reference point (e.g., TSS):

peaktools reference-point \
    <bed_file> \
    <bam_file> \
    <heatmap_output> \
    <profile_output> \
    --output <csv_output> \
    -p <num_processes>

Scale Region Analysis

Analyze peaks across scaled regions:

peaktools scale_region \
    <bed_file> \
    <bam_file> \
    <csv_output> \
    <heatmap_output> \
    <profile_output> \
    -p <num_processes>

Python Package

You can also use peaktools as a Python package:

import peaktools

# Your code here