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pydnase

Python module for the easy handling and analysis of DNase-seq data

https://github.com/jpiper/pydnase

Science Score: 23.0%

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    CITATION.cff file
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    Found 2 DOI reference(s) in README
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    3 of 7 committers (42.9%) from academic institutions
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    Low similarity (14.8%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Python module for the easy handling and analysis of DNase-seq data

Basic Info
Statistics
  • Stars: 37
  • Watchers: 6
  • Forks: 24
  • Open Issues: 15
  • Releases: 0
Created over 13 years ago · Last pushed about 7 years ago
Metadata Files
Readme Changelog License

README.rst 

================================================
pyDNase - a library for analyzing DNase-seq data
================================================


.. image:: https://travis-ci.org/jpiper/pyDNase.svg?branch=master
    :target: https://travis-ci.org/jpiper/pyDNase
.. image:: https://coveralls.io/repos/jpiper/pyDNase/badge.svg?branch=master&service=github
    :target: https://coveralls.io/github/jpiper/pyDNase?branch=master

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

pyDNase is a suite of tools for analysing DNase-seq data - pyDNase comes with several analysis scripts covering several common use cases of DNase-seq analysis, and also an implementation of the Wellington, Wellington 1D, and Wellington-boostrap footprinting algorithms. 

An easy-to-understand DNase-seq footprinting tutorial can be found  `here `__ and full documentation can be accessed `here `__

API
---

Many people currently analyzing DNase-seq data are using tools designed for ChIP-seq work, but may be inappropriate for DNase-seq data where one is less interested in the overlaps of sequenced fragments, but the site at which the cut occurs (the 5' most end of the aligned sequence fragment).

pyDNase has an underlying API to interface with a sorted and indexed BAM file from a DNase-seq experiment, allowing efficient and easy random access of DNase-seq cut data from any genomic location, e.g.

    >>> import pyDNase
    >>> reads = pyDNase.BAMHandler(pyDNase.example_reads())
    >>> reads["chr6,170863500,170863532,+"]
    {'+': [0,0,0,1,0,0,1,1,2,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,1,1,0,0,0,1],
     '-': [0,10,1,0,1,0,4,9,0,1,0,2,1,0,0,0,0,0,3,0,6,3,0,0,0,1,1,1,3,0,3,6]}

Querying the ``BAMHandler`` object returns a dictionary containing lists with DNase cut counts on the positive reference strand (+), and cuts on the negative reference strand (-). pyDNase efficiently caches the cut data queried, so that multiple requests from the same genomic locations do not require repeated lookups from the BAM file (this can be disabled). See the full documentation for full details.

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

to install pyDNase, run::

    $ pip install pyDNase

for full documentation go to: http://pythonhosted.org/pyDNase/

Support
-------

If you're having any troubles, please send an email to `j.piper@me.com` and I'll do my best to help you out. If you notice any bugs, then please raise an issue over at the github repo. If you require more formal training on the analysis of DNase-seq or ATAC-seq data, I am available for consultancy. Likewise, if you are a commercial entity looking for a support contract, please get in touch.

Contributions
-------------
I highly encourage contributions! This is my first software development project - send any pull requests this way. I'm particularly interested in cool analysis scripts that anyone has written.

Reference
---------

.. note ::
    If you use pyDNase or the Wellington algorithm in your work, please cite the following papers.
    
    Piper et al. 2013. *Wellington: A novel method for the accurate identification of digital genomic footprints from DNase-seq data*, Nucleic Acids Research 2013; doi: 10.1093/nar/gkt850

    Piper et al. 2015. *Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors*, BMC Genomics 2015; doi:10.1186/s12864-015-2081-4 

License
-------

Copyright (C) 2015 Jason Piper. This work is licensed under the MIT license, see ``LICENCE.TXT`` for details. If you require the use of this software under a difference license, please email me at `j.piper@me.com`.

Owner

  • Name: jpiper
  • Login: jpiper
  • Kind: user
  • Location: UK

Data Engineer

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 160
  • Total Committers: 7
  • Avg Commits per committer: 22.857
  • Development Distribution Score (DDS): 0.175
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jason Piper j****r@m****m 132
Jason Piper j****r@h****m 20
dpryan79 d****9@g****m 4
Roman Briskine r****e@g****m 1
Bill Greenwald b****d@u****u 1
J. Steen Hoyer j****r@w****u 1
Aleksander Jankowski a****k@m****l 1
Committer Domains (Top 20 + Academic)
mimuw.edu.pl: 1 wustl.edu: 1 ucsd.edu: 1 humanlongevity.com: 1 me.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 38
  • Total pull requests: 10
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 28
  • Total pull request authors: 7
  • Average comments per issue: 1.74
  • Average comments per pull request: 3.4
  • Merged pull requests: 8
  • 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
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Top Authors
Issue Authors
  • jpiper (7)
  • blacktanktop (2)
  • KRSBar (2)
  • billgreenwald (2)
  • bheavner (2)
  • Honchkrow (1)
  • jnyhuis (1)
  • akmorrow13 (1)
  • SaideepGona (1)
  • Xparx (1)
  • dpryan79 (1)
  • Wanvdphelys (1)
  • kerrybubb (1)
  • glucksfall (1)
  • Zefeng-Wu (1)
Pull Request Authors
  • jpiper (3)
  • dpryan79 (2)
  • brisk022 (1)
  • billgreenwald (1)
  • sirusb (1)
  • ajank (1)
  • jshoyer (1)
Top Labels
Issue Labels
enhancement (2)
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Packages

  • Total packages: 3
  • Total downloads:
    • pypi 166 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 19
  • Total maintainers: 1
proxy.golang.org: github.com/jpiper/pyDNase
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 11 months ago
proxy.golang.org: github.com/jpiper/pydnase
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 11 months ago
pypi.org: pydnase

DNase-seq analysis library

  • Versions: 17
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 166 Last month
Rankings
Forks count: 7.8%
Dependent packages count: 10.0%
Stargazers count: 10.7%
Average: 12.8%
Downloads: 14.0%
Dependent repos count: 21.7%
Maintainers (1)
jpiper
Last synced: 11 months ago

Dependencies

setup.py pypi
  • Cython *
  • Not *
  • clint *
  • matplotlib *
  • numpy *
  • pysam *