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# HybridExpress <img src="man/figures/logo.png" align="right" height="139" alt="" />
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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)](https://doi.org/10.1186/1741-7007-7-18). The 12
expression categories proposed by [Rapp et
al. (2009)](https://doi.org/10.1186/1741-7007-7-18) 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](http://cran.r-project.org/). Then install `HybridExpress` from
[Bioconductor](http://bioconductor.org/) using the following code:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("HybridExpress")
```
And the development version from
[GitHub](https://github.com/almeidasilvaf/HybridExpress) 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,
#> <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](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/3.18/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/HybridExpress) is
automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
This package was developed using
*[biocthis](https://bioconductor.org/packages/3.18/biocthis)*.
