Metadata-Version: 2.3
Name: peaktools-wrc
Version: 1.1.0
Summary: 
License: MIT
Keywords: bioinformatics,peak-calling
Author: wurucheng123
Author-email: wurucheng@pumc.edu.cn
Requires-Python: >=3.12
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: fire (>=0.7.1,<0.8.0)
Requires-Dist: pysam (>=0.23.3,<0.24.0)
Requires-Dist: seaborn (>=0.13.2,<0.14.0)
Description-Content-Type: text/markdown

# Peaktools
## About peaktools
Brief: **peaktools**, a python **package** & **command-line tool** for **peak visualization** from ChIP-seq and ATAC-seq data.

Home: https://github.com/wurucheng123/peaktools

License: MIT License

## About Author
Name: Ru-Cheng Wu | Email: wrc1953@outlook.com

## Installation
You can install peaktools via pip:
```bash
pip install peaktools-wrc
```
## Usage
To use peaktools visualize peaks in a reference point:
```bash
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
```
To use peaktools visualize peaks in a scale region:
```bash
peaktools scale_region \
    hg38_refseq_gene_TSS_TES.protein_only.chr21.bed \
    ./bam_files/293.ChIP.H3K4me3.rep1.ENCFF449FCR.bam \
    signal_H3K4me3.ScaleRegion.csv \
    ./H3K4me3_heatmap.pdf ./H3K4me3_profile.pdf -p 4
```
