DOI: 10.18129/B9.bioc.syntenet  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see syntenet.

Inference And Analysis Of Synteny Networks

Bioconductor version: 3.17

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: Fabrício Almeida-Silva [aut, cre] , Tao Zhao [aut] , Kristian K Ullrich [aut] , Yves Van de Peer [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at>

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biocViews ComparativeGenomics, FunctionalGenomics, GraphAndNetwork, Network, NetworkInference, Phylogenetics, Software, SystemsBiology, WholeGenome
Version 1.2.4
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License GPL-3
Depends R (>= 4.2)
Imports Rcpp (>= 1.0.8), BiocParallel, GenomicRanges, rlang, Biostrings, rtracklayer, utils, methods, igraph, stats, grDevices, RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph, networkD3
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Suggests BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2
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