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syntenet

This is the development version of syntenet; for the stable release version, see syntenet.

Inference And Analysis Of Synteny Networks


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("syntenet")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("syntenet")
Inference and Analysis of Synteny Networks HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ComparativeGenomics, FunctionalGenomics, GraphAndNetwork, Network, NetworkInference, Phylogenetics, Software, SystemsBiology, WholeGenome
Version 1.5.0
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
See More
Suggests BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2
Linking To Rcpp, testthat
Enhances
Depends On Me
Imports Me doubletrouble
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package syntenet_1.5.0.tar.gz
Windows Binary syntenet_1.5.0.zip
macOS Binary (x86_64) syntenet_1.5.0.tgz
macOS Binary (arm64) syntenet_1.5.0.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/
Package Downloads Report Download Stats