This is the released version of syntenet; for the devel version, see syntenet.
Inference And Analysis Of Synteny NetworksBioconductor version: Release (3.21)
syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.
Author: FabrÃcio Almeida-Silva [aut, cre] ORCID: 0000-0002-5314-2964 , Tao Zhao [aut] ORCID: 0000-0001-7302-6445 , Kristian K Ullrich [aut] ORCID: 0000-0003-4308-9626 , Yves Van de Peer [aut] ORCID: 0000-0003-4327-3730
Maintainer: FabrÃcio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
Citation (from within R, entercitation("syntenet")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("syntenet")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("syntenet")Follow Installation instructions to use this package in your R session.
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