knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
This package contains multiple vignettes that illustrate the simple ways of employing the network comparison methods 'Netdis', 'NetEmd' and their variants (e.g. `Netdis-GP'), and also the large flexibility of these methodologies. The following is a list of the available vignettes:
Simple and quick (default) usage 1: pairwise comparisons. For comparisons between two networks.
Simple and quick (default) usage 2: precomputed properties. For comparisons that use pre-computed properties. This may be useful if a user specific property is to be used; but also when the user wants to save computation time in a setting of multiple comparisons against the same network.
Simple and quick (default) usage 3: many to many comparisons. User friendly options to retrieve all pairwise comparisons among a set of $n$ networks.
"Netdis: Protein interaction networks". Shows a potential application of Netdis for real world protein interaction networks.
"NetEmd: World trade networks". Shows a potential application of NetEmd using world trade networks.
"Netdis: customizations". Shows general parameter changes of Netdis.
"Netdis: step by step". Shows a breakdown of the Netdis computation.
"Netdis-GP: step by step". Shows a breakdown of the Netdis-GP variant computation.
W. Ali, T. Rito, G. Reinert, F. Sun, and C. M. Deane. Alignment-free protein interaction network comparison. Bioinformatics, 30:i430–i437, 2014.
A. E. Wegner, L. Ospina-Forero, R. E. Gaunt, C. M. Deane, and G. Reinert. Identifying networks with common organizational principles. Journal of Complex networks, 2017.
L. Ospina-Forero, C. M. Deane, and G. Reinert. Assessment of model fit via network comparison methods based on subgraph counts. Journal of Complex Networks, page cny017, August 2018.
F. Picard, J.-J. Daudin, M. Koskas, S. Schbath, and S. Robin. Assessing the exceptionality of network motifs. Journal of Computational Biology, 15(1):1–20, 2008.
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