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DESCRIPTION
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DESCRIPTION
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Package: AligNet
Type: Package
Title: Tool to Analyze PPI Networks and Align Networks using AligNet Algorithm
algorithm
Version: 0.6
Date: 2015-11-20
Authors@R: c(person("Adria", "Alcala", role=c("aut","cre"), email =
"adria.alcala@uib.es"),person("Ricardo", "Alberich",
role="aut"),person("Merce","Llabres",
role="aut"),person("Francesc","Rossello",
role="aut"),person("Gabriel","Valiente", role="aut"))
Maintainer: Adria Alcala <adria.alcala@uib.es>
Description: This package implements AligNet, a novel alignment algorithm aimed
to obtain a global pairwise alignment of protein interaction networks, but
also, to analyze the networks from the topological study of their
modularization. AligNet obtains biological meaningful modules of a PPI
network considering an overlapping clustering based on a similarity score
between pairs of proteins, which is defined considering both their
topological and their biological information. The analysis of the networks
consists of the study of some topological features of the modules. Then,
AligNet is able to obtained a well defined global pairwise alignment from
the local alignment of the modules, which improved the results of the
previous algorithms in the tests that we performed. The novelty of our tool
AligNet is that on one hand, it is a tool for the global pairwise alignment
of protein interaction networks and, on the other hand, it is also a tool
for the analysis of a protein interaction network. The main advantage of
AligNet, is that the analysis of the networks to be aligned is performed
before the alignment itself. This entails that before computing the
alignment we know wether the networks are well studied or, on the contrary,
we can infer that they are not. Since the goodness of the alignment is
related to the goodness of the networks, knowing in advance the networks
accuracy is important to understand the final alignment.
Depends:
R (>= 2.14.1),
igraph (>= 0.7.1),
data.table (>= 1.9.2),
Matrix (>= 1.1-4)
VignetteBuilder: knitr
Suggests:
knitr (>= 1.6),
rmarkdown
Imports:
parallel (>= 3.1.2),
plot3D (>= 1.0-2),
clue (>= 0.3-48),
plyr (>= 1.8.1),
lpSolveAPI (>= 5.5.2.0-14)
License: GPL-3
SystemRequirements: python, java
LazyData: true
Packaged: 2015-06-11 13:55:51 UTC; adria
Author: Adria Alcala [aut, cre],
Ricardo Alberich [aut],
Merce Llabres [aut],
Francesc Rossello [aut],
Gabriel Valiente [aut]
RoxygenNote: 5.0.1