Metadata-Version: 2.4
Name: MACS3
Version: 3.1.0
Summary: Model Based Analysis for ChIP-Seq data
Author-email: Tao Liu <vladimir.liu@gmail.com>, Philippa Doherty <Philippa.Doherty@RoswellPark.org>
License-Expression: BSD-3-Clause
Project-URL: Homepage, https://macs3-project.github.io/MACS/
Project-URL: Documentation, https://macs3-project.github.io/MACS/
Project-URL: Repository, https://github.com/macs3-project/MACS/
Project-URL: Issues, https://github.com/macs3-project/MACS/issues
Project-URL: Changelog, https://github.com/macs3-project/MACS/blob/master/ChangeLog
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Programming Language :: Cython
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: MACS3/IO/libdeflate/COPYING
License-File: MACS3/Signal/NUMPY_LICENSE.txt
License-File: MACS3/fermi-lite/LICENSE.txt
License-File: MACS3/fermi-lite/lib/COPYING
Requires-Dist: numpy>=1.25
Requires-Dist: scipy>=1.12
Requires-Dist: pandas>=2.0
Requires-Dist: anndata>=0.10
Requires-Dist: hmmlearn>=0.3.2
Requires-Dist: scikit-learn>=1.3
Dynamic: license-file

# MACS: Model-based Analysis for ChIP-Seq

![Status](https://img.shields.io/pypi/status/macs3.svg) ![License](https://img.shields.io/github/license/macs3-project/MACS) ![Programming languages](https://img.shields.io/github/languages/top/macs3-project/MACS) [![CI x64](https://github.com/macs3-project/MACS/actions/workflows/build-and-test-MACS3-x64.yml/badge.svg)](https://github.com/macs3-project/MACS/actions/workflows/build-and-test-MACS3-x64.yml) [![CI non x64](https://github.com/macs3-project/MACS/actions/workflows/build-and-test-MACS3-non-x64.yml/badge.svg)](https://github.com/macs3-project/MACS/actions/workflows/build-and-test-MACS3-non-x64.yml) [![CI Mac OS](https://github.com/macs3-project/MACS/actions/workflows/build-and-test-MACS3-macos.yml/badge.svg)](https://github.com/macs3-project/MACS/actions/workflows/build-and-test-MACS3-macos.yml)

[![PyPI
download](https://img.shields.io/pypi/dm/macs3?label=pypi%20downloads)](https://pypistats.org/packages/macs3)

Latest Release:
* Github: [![Github Release](https://img.shields.io/github/v/release/macs3-project/MACS)](https://github.com/macs3-project/MACS/releases)
* PyPI: [![PyPI Release](https://img.shields.io/pypi/v/macs3.svg)](https://pypi.org/project/MACS3/)
* Bioconda:[![Bioconda Badge](https://anaconda.org/bioconda/macs3/badges/version.svg)](https://anaconda.org/bioconda/macs3)
* Debian Med: [![Debian Stable](https://img.shields.io/debian/v/macs/stable?label=debian%20stable)](https://packages.debian.org/stable/macs)[![Debian Unstable](https://img.shields.io/debian/v/macs/sid?label=debian%20sid)](https://packages.debian.org/sid/macs)


## Introduction

With the improvement of sequencing techniques, chromatin
immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
is getting popular to study genome-wide protein-DNA interactions. To
address the lack of powerful ChIP-Seq analysis method, we presented
the **M**odel-based **A**nalysis of **C**hIP-**S**eq (MACS), for
identifying transcript factor binding sites. MACS captures the
influence of genome complexity to evaluate the significance of
enriched ChIP regions and MACS improves the spatial resolution of
binding sites through combining the information of both sequencing tag
position and orientation. MACS can be easily used for ChIP-Seq data
alone, or with a control sample with the increase of
specificity. Moreover, as a general peak-caller, MACS can also be
applied to any "DNA enrichment assays" if the question to be asked is
simply: *where we can find significant reads coverage than the random
background*.

Please find MACS3 documentations through [MACS3
website](https://macs3-project.github.io/MACS/).

## What's new in MACS 3.1.0

- **Major `callpeak` speedup:** Jacob Schreiber's auto-optimize work
  (PR #756) measured 41–64× faster runs across four default workflows (BAM,
  FRAG, BAM with control, and BAMPE). The speedup varies by workload, and
  large inputs can use more peak memory.
- Added `--threads` to supported commands to set a per-run CPU budget.
  `MACS3_NUM_THREADS` can provide a default, and Python callers can pass an
  execution policy through the public API.
- Added `--process-backend {auto,serial}` to `callpeak` and `callvar`.
- Fixed automatic duplicate filtering so control reads use the control's
  own duplicate threshold.
- Corrected lower-tail Poisson probabilities for very large expected counts.
- Improved handling of incomplete inputs: final FRAG records no longer need a
  trailing newline, and truncated BAM alignment records are rejected.
- Improved reliability when peak-calling workers or concurrent operations
  fail, including cleanup of temporary data.

See the [command-line documentation](https://macs3-project.github.io/MACS/)
for command options and the [ChangeLog](ChangeLog) for release details.

Thanks to Jacob Schreiber for the auto-optimize work (PR #755, #756); Cindy
Krafft for the duplicate-threshold and Poisson fixes (PR #753, #777) and
p-value documentation (PR #789); Michael R. Crusoe for spelling fixes
(PR #754); and Apoorva Garg for the native aarch64 CI contribution (PR #793).

## Contribute

Please read our [CODE OF CONDUCT](CODE_OF_CONDUCT.md) and [How to
contribute](CONTRIBUTING.md) documents. If you have any questions,
suggestion/ideas, or just want to have conversions with developers and
other users in the community, we recommend using the [MACS
Discussions](https://github.com/macs3-project/MACS/discussions)
instead of posting to our
[Issues](https://github.com/macs3-project/MACS/issues) page.

## Support MACS3

I maintain MACS3 in my spare time. If you find the project useful and
would like to support its continued development, you can
[![Buy Me a Coffee](https://img.shields.io/badge/Buy_Me_a_Coffee-support-FFDD00?style=for-the-badge&logo=buy-me-a-coffee&logoColor=000000)](https://buymeacoffee.com/taoliu). Your contribution
will help cover my ever-growing consumption of coffee and tokens.

## Ackowledgement

MACS3 project is sponsored by [![CZI's Essential Open Source Software for Science](https://chanzuckerberg.github.io/open-science/badges/CZI-EOSS.svg)](https://czi.co/EOSS) through EOSS2 (2020-2022) and EOSS4 (2021-2025). And we particularly want to thank the user community for their supports, feedbacks and contributions over the years.

## Citation

For MACS version 2 and 3, please cite our 2026 paper [MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics](https://academic.oup.com/gpb/advance-article/doi/10.1093/gpbjnl/qzag097/8802115)

If you are using MACS version 1, please cite our 2008 paper [Model-based Analysis of ChIP-Seq
(MACS)](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137)

## Note

Now the default branch of MACS3 has been renamed to 'main'. If you are still using old 'master' branch in your cloned Git repository for MACS3, please use the following command to rename it:

```
git branch -m master main
git fetch origin
git branch -u origin/main main
git remote set-head origin -a
```
