<!-- 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. Duplicates can be classified using four different classification schemes, which increase the complexity and level of details in a stepwise manner. The classification schemes and the duplication modes they can classify are: | Scheme | Duplication modes | |:---------|:---------------------------| | binary | SD, SSD | | standard | SD, TD, PD, DD | | extended | SD, TD, PD, TRD, DD | | full | SD, TD, PD, rTRD, dTRD, DD | *Legend:* **SD**, segmental duplication. **SSD**, small-scale duplication. **TD**, tandem duplication. **PD**, proximal duplication. **TRD**, transposon-derived duplication. **rTRD**, retrotransposon-derived duplication. **dTRD**, DNA transposon-derived duplication. **DD**, dispersed duplication. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned to a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., $K_a$, $K_s$ and their ratios $\frac{K_a}{K_s}$) 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 1.3.0, #> <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 1.3.0}, #> 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/3.17/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/3.17/biocthis)*.