nettools-package: A Network Comparison Framework
In filosi/nettools: A Network Comparison Framework

Description Details Author(s) References See Also

This package provides a collection of network inference methods for co-expression networks, quantitative network distances and a novel framework for network stability analysis.

Summary:

Package:	nettools
Type:	Package
Version:	1.0.4
Date:
Depends: R (>= 2.14.1), methods Imports: WGCNA, minet, rootSolve, dtw, Matrix, parallel, minerva, Rcpp, combinat, igraph, c3net, bc3net, R.utils License: CC BY-NC-SA 4.0

Michele Filosi [aut, cre], Roberto Visintainer [aut], Samantha Riccadonna [aut], Giuseppe Jurman [ctb], Cesare Furlanello [ctb]
Maintainer: Michele Filosi <filosi@fbk.eu>

M. Filosi, R. Visintainer, S. Riccadonna, G. Jurman, C. Furlanello (2014) Stability Indicators in Network Reconstruction, PLOSONE

A. Sole-Ribalta, M. De Domenico, N. E. Kouvaris, A. Diaz-Guilera, S. gomez, A. Arenas Spectral Properties of the Laplacian of multiplex networks, 2013, arXiv:1307.2090v1

P. Langfelder, S. Horvath (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008, 9:559

P. E. Meyer, F. Lafitte, G. Bontempi (2008). MINET: An open source R/Bioconductor Package for Mutual Information based Network Inference. BMC Bioinformatics. http://www.biomedcentral.com/1471-2105/9/461

D. Albanese, M.Filosi, R. Visintainer, S. Riccadonna, G. Jurman, C. Furlanello (2012). minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers, Bioinformatics 2012. http://minepy.readthedocs.io/en/latest/

D. Reshef, Y. Reshef, H. Finucane, S. Grossman, G. McVean, P. Turnbaugh, E. Lander, M. Mitzenmacher, P. Sabeti. (2011) Detecting novel associations in large datasets. Science 334, 6062

http://www.exploredata.net

(SOM: Supplementary Online Material at http://www.sciencemag.org/content/suppl/2011/12/14/334.6062.1518.DC1)

Further information on specific functions for inferring the adjacency matrix could be found in WGCNA, minerva and minet.

filosi/nettools documentation built on May 28, 2019, 8:38 p.m.