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manorm

A robust model for quantitative comparison of ChIP-Seq data sets.

https://github.com/shao-lab/manorm

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary

Keywords

bioinformatics chip-seq differential-expression ngs normalization
Last synced: 6 months ago · JSON representation

Repository

A robust model for quantitative comparison of ChIP-Seq data sets.

Basic Info
  • Host: GitHub
  • Owner: shao-lab
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Homepage: http://manorm.readthedocs.io/
  • Size: 6.87 MB
Statistics
  • Stars: 21
  • Watchers: 4
  • Forks: 5
  • Open Issues: 2
  • Releases: 0
Topics
bioinformatics chip-seq differential-expression ngs normalization
Created over 8 years ago · Last pushed almost 6 years ago
Metadata Files
Readme Changelog License

README.rst 

MAnorm
======

|github-actions| |Documentation Status| |pypi| |pyversion| |install with bioconda| |codecov| |license|

.. |github-actions| image:: https://github.com/shao-lab/MAnorm/workflows/Python%20package/badge.svg
   :target: https://github.com/shao-lab/MAnorm/actions
.. |Documentation Status| image:: https://readthedocs.org/projects/manorm/badge/?version=latest
   :target: http://manorm.readthedocs.io/en/latest/?badge=latest
.. |pypi| image:: https://img.shields.io/pypi/v/MAnorm.svg
   :target: https://pypi.org/project/MAnorm/
.. |pyversion| image:: https://img.shields.io/pypi/pyversions/MAnorm.svg
   :target: https://pypi.org/project/MAnorm/
.. |install with bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
   :target: http://bioconda.github.io/recipes/manorm/README.html
.. |codecov| image:: https://codecov.io/gh/shao-lab/MAnorm/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/shao-lab/MAnorm
.. |license| image:: https://img.shields.io/pypi/l/MAnorm.svg
   :target: https://github.com/shao-lab/MAnorm/blob/master/LICENSE

Introduction
------------

ChIP-Seq is widely used to characterize genome-wide binding patterns of
transcription factors and other chromatin-associated proteins. Although
comparison of ChIP-Seq data sets is critical for understanding cell
type-dependent and cell state-specific binding, and thus the study of
cell-specific gene regulation, few quantitative approaches have been
developed.

Here, we present a simple and effective method, MAnorm, for quantitative
comparison of ChIP-Seq data sets describing transcription factor binding
sites and epigenetic modifications. The quantitative binding differences
inferred by MAnorm showed strong correlation with both the changes in
expression of target genes and the binding of cell type-specific
regulators.

Citation
--------

`Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model for quantitative comparison of
ChIP-Seq data sets. Genome biology. 2012 Mar 16;13(3):R16.
`__

Documentation
-------------

To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io

Installation
------------

The latest release of MAnorm is available at `PyPI `__:

::

    $ pip install manorm

Or you can install MAnorm via conda:

::

    $ conda install -c bioconda manorm

Galaxy Installation
-------------------

MAnorm is also available on Galaxy_, you can incorporate MAnorm into your own Galaxy instance.

Please search and install MAnorm via the `Galaxy Tool Shed`_.

.. _Galaxy: https://galaxyproject.org
.. _`Galaxy Tool Shed`: https://toolshed.g2.bx.psu.edu/view/haydensun/manorm

Basic Usage
-----------

::

    $ manorm --p1 sample1_peaks.bed --p2 sample2_peaks.bed --r1 sample1_reads.bed --r2 sample2_reads.bed
    --n1 name1 --n2 name2 -o output_dir

**Note:** Using -h/--help for the details of all arguments.

License
-------

`BSD 3-Clause
License `__

GitHub Events

Total
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 145
  • Total Committers: 2
  • Avg Commits per committer: 72.5
  • Development Distribution Score (DDS): 0.083
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
haydensun h****n@h****m 133
haydensun s****o@p****n 12
Committer Domains (Top 20 + Academic)
picb.ac.cn: 1

Issues and Pull Requests

Last synced: about 2 years ago

All Time
  • Total issues: 22
  • Total pull requests: 2
  • Average time to close issues: 3 months
  • Average time to close pull requests: 14 minutes
  • Total issue authors: 17
  • Total pull request authors: 1
  • Average comments per issue: 2.45
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • AntonioAhn (3)
  • ckntav (2)
  • michael-kotliar (2)
  • chiefcat (2)
  • a091601 (1)
  • crg-eilslabs (1)
  • dsytan (1)
  • AlicePsyche (1)
  • gaoyishu (1)
  • ishtiaqueh (1)
  • Yippee0 (1)
  • YannVRB (1)
  • yysheep2020 (1)
  • Rseq (1)
  • liehu232 (1)
Pull Request Authors
  • hongduosun (2)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 17 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
pypi.org: manorm

A robust model for quantitative comparison of ChIP-Seq data sets

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 17 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 13.3%
Forks count: 15.3%
Average: 18.2%
Dependent repos count: 21.7%
Downloads: 30.5%
Maintainers (1)
haydensun
Last synced: 6 months ago

Dependencies

setup.py pypi
  • matplotlib >=3.0.0
  • numpy *
  • pysam >=0.15.0
  • scikit-learn >=0.21.0