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Inference And Analysis Of Synteny Networks

Bioconductor version: Release (3.18)

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 hotmail.com>

Citation (from within R, enter citation("syntenet")):


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Inference and Analysis of Synteny Networks HTML R Script
Reference Manual PDF


biocViews ComparativeGenomics, FunctionalGenomics, GraphAndNetwork, Network, NetworkInference, Phylogenetics, Software, SystemsBiology, WholeGenome
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements
URL https://github.com/almeidasilvaf/syntenet
Bug Reports https://support.bioconductor.org/t/syntenet
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Suggests BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2
Linking To Rcpp, testthat
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Imports Me doubletrouble
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Package Archives

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Source Package syntenet_1.4.0.tar.gz
Windows Binary syntenet_1.4.0.zip
macOS Binary (x86_64) syntenet_1.4.0.tgz
macOS Binary (arm64) syntenet_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/syntenet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/syntenet
Bioc Package Browser https://code.bioconductor.org/browse/syntenet/
Package Short Url https://bioconductor.org/packages/syntenet/
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