https://github.com/almeidasilvaf/hybridexpress
An R package for comparative transcriptomic analyses of hybrids and their progenitors
https://github.com/almeidasilvaf/hybridexpress
gene-expression hybrid polyploidy rna-seq transcriptomics
Last synced: 4 months ago
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An R package for comparative transcriptomic analyses of hybrids and their progenitors
- Host: GitHub
- URL: https://github.com/almeidasilvaf/hybridexpress
- Owner: almeidasilvaf
- Created: 2023-10-17T06:33:02.000Z (over 2 years ago)
- Default Branch: devel
- Last Pushed: 2024-09-05T06:27:48.000Z (almost 2 years ago)
- Last Synced: 2025-09-28T22:25:08.092Z (9 months ago)
- Topics: gene-expression, hybrid, polyploidy, rna-seq, transcriptomics
- Language: R
- Homepage: https://almeidasilvaf.github.io/HybridExpress
- Size: 19.2 MB
- Stars: 14
- Watchers: 2
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Support: .github/SUPPORT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# HybridExpress 
[](https://github.com/almeidasilvaf/HybridExpress/issues)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/rworkflows.devel.yml)
[](https://app.codecov.io/gh/almeidasilvaf/HybridExpress?branch=devel)
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 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("HybridExpress")
```
And the development version from [GitHub](https://github.com/almeidasilvaf/HybridExpress) with:
```{r 'install_dev', eval = FALSE}
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 'citation', eval = requireNamespace('HybridExpress')}
print(citation('HybridExpress'), bibtex = TRUE)
```
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 `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://almeidasilvaf.github.io/HybridExpress) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.