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<!-- is generated from README.Rmd. Please edit that file --> # syntenet <img src="man/figures/logo.png" align="right" height="138" /> <!-- badges: start --> [![GitHub issues](]( [![Lifecycle: stable](]( [![R-CMD-check-bioc](]( [![Codecov test coverage](]( <!-- badges: end --> The goal of `syntenet` is to infer synteny networks from whole-genome protein sequence data and analyze them. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: - **Synteny detection** using a native implementation of the [MCScanX algorithm](, a C++ program that has been modified and ported to R with Rcpp. This way, users do not need to install MCScanX beforehand, because `syntenet` has its own implementation of the same algorithm. - **Synteny network inference** by treating anchor pairs as edges of a graph; - **Network clustering** using the Infomap algorithm; - **Phylogenomic profiling**, which consists in identifying which species contain which clusters. This analysis can reveal highly conserved synteny clusters and taxon-specific ones (e.g., family- and order-specific clusters); - **Microsynteny-based phylogeny reconstruction** with maximum likelihood, which can be achieved by inferring a phylogeny from a binary matrix of phylogenomic profiles with IQTREE. ## Installation instructions Get the latest stable `R` release from [CRAN]( Then install `syntenet` from [Bioconductor]( using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("syntenet") ``` And the development version from [GitHub]( with: ``` r BiocManager::install("almeidasilvaf/syntenet") ``` ## Citation Below is the citation output from using `citation('syntenet')` in R. Please run this yourself to check for any updates on how to cite **syntenet**. ``` r print(citation('syntenet'), bibtex = TRUE) #> #> To cite syntenet in publications, use: #> #> Almeida-Silva, F., Zhao, T., Ullrich, K.K., Schranz, M.E. and Van de #> Peer, Y. syntenet: an R/Bioconductor package for the inference and #> analysis of synteny networks. Bioinformatics, 39(1), p.btac806. #> (2023). #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {syntenet: an R/Bioconductor package for the inference and analysis of synteny networks}, #> author = {Fabricio Almeida-Silva and Tao Zhao and Kristian K. Ullrich and M. Eric Schranz and Yves {Van de Peer}}, #> journal = {Bioinformatics}, #> year = {2023}, #> volume = {39}, #> number = {1}, #> pages = {btac806}, #> url = {}, #> doi = {10.1093/bioinformatics/btac806}, #> } ``` Please note that `syntenet` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package. ## Code of Conduct Please note that the `syntenet` project is released with a [Contributor Code of Conduct]( By contributing to this project, you agree to abide by its terms. ## Development tools - Continuous code testing is possible thanks to [GitHub actions]( through *[usethis](*, *[remotes](*, and *[rcmdcheck](* customized to use [Bioconductor’s docker containers]( and *[BiocCheck](*. - Code coverage assessment is possible thanks to [codecov]( and *[covr](*. - The [documentation website]( is automatically updated thanks to *[pkgdown](*. - The code is styled automatically thanks to *[styler](*. - The documentation is formatted thanks to *[devtools](* and *[roxygen2](*. For more details, check the `dev` directory. This package was developed using *[biocthis](*.