syntenet

DOI: 10.18129/B9.bioc.syntenet    

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

Inference And Analysis Of Synteny Networks

Bioconductor version: Development (3.17)

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 hotmail.com>

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews	ComparativeGenomics, FunctionalGenomics, GraphAndNetwork, Network, NetworkInference, Phylogenetics, Software, SystemsBiology, WholeGenome
Version	1.1.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	GPL-3
Depends	R (>= 4.2)
Imports	Rcpp (>= 1.0.8), GenomicRanges, Biostrings, rtracklayer, utils, methods, igraph, stats, labdsv, grDevices, RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph, networkD3
LinkingTo	Rcpp, testthat
Suggests	BiocStyle, ggtree, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2
SystemRequirements
Enhances
URL	https://github.com/almeidasilvaf/syntenet
BugReports	https://support.bioconductor.org/t/syntenet
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	syntenet_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/syntenet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/syntenet
Package Short Url	https://bioconductor.org/packages/syntenet/
Package Downloads Report	Download Stats