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pyDNase

Allows users to analyse DNase-seq data. pyDNase is a suite of tools that provide several algorithms, including Wellington, a method for pairwise analysis of DNase-seq data sets, Wellington 1D, and Wellington-boostrap foot-printing. It also offers an integrated API to provide an interface with a sorted and indexed BAM file from a DNase-seq experiment. This allows an efficient and easy random access to DNase-seq cutting data from any genomic location.

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pyDNase classification

pyDNase specifications

Software type:
Framework/Library
Restrictions to use:
None
Programming languages:
Python
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface, Application programming interface
Operating system:
Unix/Linux, Mac OS
License:
GNU General Public License version 3.0
Version:
0.2.5
Maintained:
Yes

Subtools

  • Wellington

pyDNase distribution

versioning

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No versioning.

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pyDNase support

Documentation

Maintainers

  • Jason Piper <>
  • Peter Cockerill <>
  • Constanze Bonifer <>
  • Sascha Ott <>

Additional information

http://pythonhosted.org/pyDNase/

Credits

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Publications

Institution(s)

Warwick Systems Biology Centre, University of Warwick, Coventry, UK; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK; Department of Computer Science, University of Warwick, Coventry, UK

Funding source(s)

Partly supported by the Engineering and Physical Sciences Research Council (EP/P50578X/1 PhD grant) and grants from Leukaemia Lymphoma Research and the Kay Kendall Leukaemia Fund.

Link to literature

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