syntenet
This is thereleased version of syntenet; for the devel version, seesyntenet.
Inference And Analysis Of Synteny Networks
Bioconductor version: Release (3.22)
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: 0000-0002-5314-2964, Tao Zhao [aut] ORCID: 0000-0001-7302-6445, Kristian K Ullrich [aut] ORCID: 0000-0003-4308-9626, Yves Van de Peer [aut] ORCID: 0000-0003-4327-3730
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("syntenet")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("syntenet")For older versions of R, please refer to the appropriateBioconductor 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 |
| syntenet as a synteny detection tool | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics,FunctionalGenomics,GraphAndNetwork,Network,NetworkInference,Phylogenetics,Software,SystemsBiology,WholeGenome |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.2) |
| Imports | Rcpp (>= 1.0.8),BiocParallel,GenomicRanges,rlang,Biostrings, 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 |
See More
| Suggests | rtracklayer,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
FollowInstallation instructions to use this package in your R session.
| Source Package | syntenet_1.12.0.tar.gz |
| Windows Binary (x86_64) | syntenet_1.12.0.zip |
| macOS Binary (x86_64) | syntenet_1.12.0.tgz |
| macOS Binary (arm64) | syntenet_1.12.0.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 3.22 | Source Archive |