<!-- README.md is generated from README.Rmd. Please edit that file --> # doubletrouble <img src="man/figures/logo.png" align="right" height="139" /> <!-- badges: start --> [](https://github.com/almeidasilvaf/doubletrouble/issues) [](https://lifecycle.r-lib.org/articles/stages.html#stable) [](https://github.com/almeidasilvaf/doubletrouble/actions) [](https://codecov.io/gh/almeidasilvaf/doubletrouble?branch=devel) <!-- badges: end --> The major goal of `doubletrouble` is to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The simplest classification scheme has two duplication modes: 1. Whole-genome duplication (WGD); 2. Small-scale duplication (SSD) For a more detailed view of the duplication modes, users can also choose to split SSD into subcategories, so the available duplication modes will be: 1. Whole-genome duplication (WGD); 2. Tandem duplication (TD); 3. Proximal duplication (PD); 4. Transposed duplication (TRD); 5. Dispersed duplication (DD). Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks. ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `doubletrouble` from [Bioconductor](http://bioconductor.org/) using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("doubletrouble") ``` And the development version from [GitHub](https://github.com/almeidasilvaf/doubletrouble) with: ``` r BiocManager::install("almeidasilvaf/doubletrouble") ``` ## Citation Below is the citation output from using `citation('doubletrouble')` in R. Please run this yourself to check for any updates on how to cite **doubletrouble**. ``` r print(citation('doubletrouble'), bibtex = TRUE) #> #> To cite package 'doubletrouble' in publications use: #> #> Almeida-Silva F, Van de Peer Y (2022). _doubletrouble: Identification #> and classification of duplicated genes_. R package version 0.99.1, #> <https://github.com/almeidasilvaf/doubletrouble>. #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {doubletrouble: Identification and classification of duplicated genes}, #> author = {Fabrício Almeida-Silva and Yves {Van de Peer}}, #> year = {2022}, #> note = {R package version 0.99.1}, #> url = {https://github.com/almeidasilvaf/doubletrouble}, #> } ``` Please note that the `doubletrouble` 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 `doubletrouble` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/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](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through *[usethis](https://CRAN.R-project.org/package=usethis)*, *[remotes](https://CRAN.R-project.org/package=remotes)*, and *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized to use [Bioconductor’s docker containers](https://www.bioconductor.org/help/docker/) and *[BiocCheck](https://bioconductor.org/packages/3.15/BiocCheck)*. - Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and *[covr](https://CRAN.R-project.org/package=covr)*. - The [documentation website](http://almeidasilvaf.github.io/doubletrouble) is automatically updated thanks to *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*. - The code is styled automatically thanks to *[styler](https://CRAN.R-project.org/package=styler)*. - The documentation is formatted thanks to *[devtools](https://CRAN.R-project.org/package=devtools)* and *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*. For more details, check the `dev` directory. This package was developed using *[biocthis](https://bioconductor.org/packages/3.15/biocthis)*.