HybridExpress

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:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("HybridExpress")

And the development version from GitHub with:

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.

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,
#>   <https://github.com/almeidasilvaf/HybridExpress>.
#> 
#> 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 = {https://github.com/almeidasilvaf/HybridExpress},
#>   }

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.