minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers

نویسندگان

  • Davide Albanese
  • Michele Filosi
  • Roberto Visintainer
  • Samantha Riccadonna
  • Giuseppe Jurman
  • Cesare Furlanello
چکیده

UNLABELLED We introduce a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets, with the aim of a low memory footprint and ease of integration within bioinformatics pipelines. We provide the libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave and C++. The C solution reduces the large memory requirement of the original Java implementation, has good upscaling properties and offers a native parallelization for the R interface. Low memory requirements are demonstrated on the MINE benchmarks as well as on large ( = 1340) microarray and Illumina GAII RNA-seq transcriptomics datasets. AVAILABILITY AND IMPLEMENTATION Source code and binaries are freely available for download under GPL3 licence at http://minepy.sourceforge.net for minepy and through the CRAN repository http://cran.r-project.org for the R package minerva. All software is multiplatform (MS Windows, Linux and OSX).

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عنوان ژورنال:
  • Bioinformatics

دوره 29 3  شماره 

صفحات  -

تاریخ انتشار 2013