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<!-- is generated from README.Rmd. Please edit that file --> # doubletrouble <img src="man/figures/logo.png" align="right" height="139" /> <!-- badges: start --> [![GitHub issues](]( [![Lifecycle: stable](]( [![R-CMD-check-bioc](]( [![Codecov test coverage](]( <!-- 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]( Then install **doubletrouble** from [Bioconductor]( using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("doubletrouble") ``` And the development version from [GitHub]( 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, #> <>. #> #> 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 = {}, #> } ``` 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]( 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](*.