README.md

   1 # MACS: Model-based Analysis for ChIP-Seq
   2
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   4
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   6 download](https://img.shields.io/pypi/dm/macs3?label=pypi%20downloads)](https://pypistats.org/packages/macs3)
   7
   8 Latest Release:
   9 * Github: [![Github Release](https://img.shields.io/github/v/release/macs3-project/MACS)](https://github.com/macs3-project/MACS/releases)
  10 * PyPI: [![PyPI Release](https://img.shields.io/pypi/v/macs3.svg)](https://pypi.org/project/MACS3/)
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  12 * 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)
  13
  14
  15 ## Introduction
  16
  17 With the improvement of sequencing techniques, chromatin
  18 immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
  19 is getting popular to study genome-wide protein-DNA interactions. To
  20 address the lack of powerful ChIP-Seq analysis method, we presented
  21 the **M**odel-based **A**nalysis of **C**hIP-**S**eq (MACS), for
  22 identifying transcript factor binding sites. MACS captures the
  23 influence of genome complexity to evaluate the significance of
  24 enriched ChIP regions and MACS improves the spatial resolution of
  25 binding sites through combining the information of both sequencing tag
  26 position and orientation. MACS can be easily used for ChIP-Seq data
  27 alone, or with a control sample with the increase of
  28 specificity. Moreover, as a general peak-caller, MACS can also be
  29 applied to any "DNA enrichment assays" if the question to be asked is
  30 simply: *where we can find significant reads coverage than the random
  31 background*.
  32
  33 Please find MACS3 documentations through [MACS3
  34 website](https://macs3-project.github.io/MACS/).
  35
  36 ## Contribute
  37
  38 Please read our [CODE OF CONDUCT](CODE_OF_CONDUCT.md) and [How to
  39 contribute](CONTRIBUTING.md) documents. If you have any questions,
  40 suggestion/ideas, or just want to have conversions with developers and
  41 other users in the community, we recommend using the [MACS
  42 Discussions](https://github.com/macs3-project/MACS/discussions)
  43 instead of posting to our
  44 [Issues](https://github.com/macs3-project/MACS/issues) page.
  45
  46 ## Ackowledgement
  47
  48 MACS3 project is sponsored by
  49 [CZI EOSS](https://chanzuckerberg.com/eoss/). And we particularly want
  50 to thank the user community for their supports, feedbacks and
  51 contributions over the years.
  52
  53 ## Citation
  54
  55 2008: [Model-based Analysis of ChIP-Seq
  56 (MACS)](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137)
  57