minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers
minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers
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DOI：
10.1093/bioinformatics/bts707
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发表时间：
2013-02-01
期刊：
影响因子：
5.8
通讯作者：
Furlanello, Cesare
中科院分区：
文献类型：
--
作者：
Albanese, Davide;Filosi, Michele;Furlanello, Cesare
答：我们介绍了一种新的实现在ANSI C中的MINE家族的算法，用于计算最大的基于信息的措施，在大型数据集中的两个变量之间的依赖关系，其目的是一个低内存占用和易于集成的生物信息学管道。我们为Python、MATLAB、Octave和C++提供了minerva（带有R接口）和mininstance库。C解决方案减少了原始Java实现的大内存需求，具有良好的升级特性，并为R接口提供了本地并行化。在MINE基准测试以及大型（n = 1340）微阵列和Illumina GAII RNA-seq转录组学数据集上证明了低内存要求。
A: 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 (n = 1340) microarray and Illumina GAII RNA-seq transcriptomics datasets.