altingia/HybridExpress

An R package for comparative transcriptomic analyses of hybrids and their progenitors

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.