syntenet

DOI: 10.18129/B9.bioc.syntenet  

Inference And Analysis Of Synteny Networks

Bioconductor version: Release (3.16)

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 "4.2") 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.

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
Text		NEWS

Details

biocViews	ComparativeGenomics, FunctionalGenomics, GraphAndNetwork, Network, NetworkInference, Phylogenetics, Software, SystemsBiology, WholeGenome
Version	1.0.4
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	GPL-3
Depends	R (>= 4.2)
Imports	Rcpp (>= 1.0.8), GenomicRanges, rlang, Biostrings, rtracklayer, utils, methods, igraph, stats, grDevices, RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph, networkD3
LinkingTo	Rcpp, testthat
Suggests	BiocStyle, ggtree, labdsv, 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
Links To Me
Build Report

Package Archives

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

Source Package	syntenet_1.0.4.tar.gz
Windows Binary	syntenet_1.0.4.zip
macOS Binary (x86_64)	syntenet_1.0.4.tgz
macOS Binary (arm64)	syntenet_1.0.4.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
Old Source Packages for BioC 3.16	Source Archive