syntenet
This is the development version of syntenet; for the stable release version, see syntenet.
Inference And Analysis Of Synteny Networks
Bioconductor version: Development (3.24)
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>
citation("syntenet")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 |
| 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 | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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
Follow Installation instructions to use this package in your R session.
| Source Package | syntenet_1.15.0.tar.gz |
| Windows Binary (x86_64) | syntenet_1.15.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | syntenet_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | syntenet_1.15.0.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 |