peaktools documentation

peaktools is a Python package & command-line tool for peak visualization from ChIP-seq and ATAC-seq data.

Contents:

• Installation
  • Via pip
  • Via conda
  • From source
• Usage
  • Command-line Interface
  • Python Package
• API Reference
  • Core Modules

Quick Start

Install via pip:

pip install peaktools-wrc

Basic Usage

For reference point analysis:

peaktools reference-point \
    hg38_refseq_gene_TSS_TES.protein_only.chr21.bed \
    ./bam_files/K562-ATACSeq-rep1.ENCFF534DCE_chr21_chr22.bam \
    ATAC_heatmap.pdf ATAC_profile.pdf \
    --output ./signal_ATACSeq.RefPoint.csv -p 4

Indices and tables

• Index

• Module Index

• Search Page