PyPanda: a Python package for gene regulatory network reconstruction

Summary: PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of ‘omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PAN...

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Autores principales: van IJzendoorn, David G.P., Glass, Kimberly, Quackenbush, John, Kuijjer, Marieke L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079480/
https://www.ncbi.nlm.nih.gov/pubmed/27402905
http://dx.doi.org/10.1093/bioinformatics/btw422
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author van IJzendoorn, David G.P.
Glass, Kimberly
Quackenbush, John
Kuijjer, Marieke L.
author_facet van IJzendoorn, David G.P.
Glass, Kimberly
Quackenbush, John
Kuijjer, Marieke L.
author_sort van IJzendoorn, David G.P.
collection PubMed
description Summary: PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of ‘omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis. Availability and implementation: The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda. Contact: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl
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spelling pubmed-50794802016-10-26 PyPanda: a Python package for gene regulatory network reconstruction van IJzendoorn, David G.P. Glass, Kimberly Quackenbush, John Kuijjer, Marieke L. Bioinformatics Applications Notes Summary: PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of ‘omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis. Availability and implementation: The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda. Contact: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl Oxford University Press 2016-11-01 2016-07-10 /pmc/articles/PMC5079480/ /pubmed/27402905 http://dx.doi.org/10.1093/bioinformatics/btw422 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
van IJzendoorn, David G.P.
Glass, Kimberly
Quackenbush, John
Kuijjer, Marieke L.
PyPanda: a Python package for gene regulatory network reconstruction
title PyPanda: a Python package for gene regulatory network reconstruction
title_full PyPanda: a Python package for gene regulatory network reconstruction
title_fullStr PyPanda: a Python package for gene regulatory network reconstruction
title_full_unstemmed PyPanda: a Python package for gene regulatory network reconstruction
title_short PyPanda: a Python package for gene regulatory network reconstruction
title_sort pypanda: a python package for gene regulatory network reconstruction
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079480/
https://www.ncbi.nlm.nih.gov/pubmed/27402905
http://dx.doi.org/10.1093/bioinformatics/btw422
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AT quackenbushjohn pypandaapythonpackageforgeneregulatorynetworkreconstruction
AT kuijjermariekel pypandaapythonpackageforgeneregulatorynetworkreconstruction

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