syntenet
Inference And Analysis Of Synteny Networks
Bioconductor version: Release (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: FabrÃcio Almeida-Silva [aut, cre] , Tao Zhao [aut]
, Kristian K Ullrich [aut]
, Yves Van de Peer [aut]
Maintainer: FabrÃcio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("syntenet")
):
Installation
To install this package, start R (version "4.4") 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")
Inference and Analysis of Synteny Networks | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | ComparativeGenomics, FunctionalGenomics, GraphAndNetwork, Network, NetworkInference, Phylogenetics, Software, SystemsBiology, WholeGenome |
Version | 1.6.0 |
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, 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_1.6.0.tar.gz |
Windows Binary | syntenet_1.6.0.zip |
macOS Binary (x86_64) | syntenet_1.6.0.tgz |
macOS Binary (arm64) | syntenet_1.6.0.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 |
Old Source Packages for BioC 3.19 | Source Archive |