syntenet

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

Inference And Analysis Of Synteny Networks

Bioconductor version: Development (3.21)

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] (ORCID: ), Tao Zhao [aut] (ORCID: ), Kristian K Ullrich [aut] (ORCID: ), Yves Van de Peer [aut] (ORCID: )

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ComparativeGenomics, FunctionalGenomics, GraphAndNetwork, Network, NetworkInference, Phylogenetics, Software, SystemsBiology, WholeGenome
Version	1.9.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 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
System Requirements
URL	https://github.com/almeidasilvaf/syntenet
Bug Reports	https://support.bioconductor.org/t/syntenet

Suggests	BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2, networkD3
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_1.9.0.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser	https://code.bioconductor.org/browse/syntenet/
Package Short Url	https://bioconductor.org/packages/syntenet/
Package Downloads Report	Download Stats