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<!-- is generated from README.Rmd. Please edit that file --> # HybridExpress <img src="man/figures/logo.png" align="right" height="139" alt="" /> <!-- badges: start --> [![GitHub issues](]( [![Lifecycle: stable](]( [![check-bioc](]( [![Codecov test coverage](]( <!-- badges: end --> The goal of `HybridExpress` is to perform comparative transcriptomic analyses of hybrids relative to their progenitor species (a.k.a. *experimental trios*). The package features: 1. **Calculation of midparent expression values**, which are *in silico* samples obtained from the mean, sum, or weighted mean of random sample pairs from each parent; 2. **Exploratory analyses of sample grouping** with PCA plots and heatmaps of hierarchically-clustered pairwise sample correlations; 3. **Identification of differentially expressed genes** between hybrids and their progenitor species, hybrids and midparent values, and the two parents. If spike-in standards are available, `HybridExpress` uses them to normalize the count data by transcriptome size; 4. **Classification of genes in expression-based categories and classes** based on [Rapp et al. (2009)]( The 12 expression categories proposed by [Rapp et al. (2009)]( are grouped into 5 major classes (transgressive up-regulation, transgressive down-regulation, additivity, expression-level dominance toward parent 1, and expression-level dominance toward parent 2); 5. **Functional analyses** through the identification of overrepresented functional terms for gene sets of interest. ## Installation instructions Get the latest stable `R` release from [CRAN]( Then install `HybridExpress` from [Bioconductor]( using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("HybridExpress") ``` And the development version from [GitHub]( with: ``` r BiocManager::install("almeidasilvaf/HybridExpress") ``` ## Citation Below is the citation output from using `citation('HybridExpress')` in R. Please run this yourself to check for any updates on how to cite **HybridExpress**. ``` r print(citation('HybridExpress'), bibtex = TRUE) #> To cite package 'HybridExpress' in publications use: #> #> Almeida-Silva F, Prost-Boxoen L, Van de Peer Y (2023). #> _HybridExpress: Comparative analysis of RNA-seq data for hybrids and #> their progenitors_. R package version 0.99.0, #> <>. #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {HybridExpress: Comparative analysis of RNA-seq data for hybrids and their progenitors}, #> author = {Fabricio Almeida-Silva and Lucas Prost-Boxoen and Yves {Van de Peer}}, #> year = {2023}, #> note = {R package version 0.99.0}, #> url = {}, #> } ``` Please note that the `HybridExpress` 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 `HybridExpress` 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 documentation is formatted thanks to *[devtools](* and *[roxygen2](*. This package was developed using *[biocthis](*.