title: PyPanda: a Python package for gene regulatory network reconstruction.
abstract: 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.
  
  
  
  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.
authors.affiliation: Department of Pathology, Leiden University Medical Center, 2300RC Leiden, The Netherlands.
authors.forename: David G P
authors.initials: DG
authors.lastname: van IJzendoorn
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Glass
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
authors.forename: Marieke L
authors.initials: ML
authors.lastname: Kuijjer
mesh_terms: D000818:Animals; D053263:Gene Regulatory Networks; D012984:Software