https://github.com/eolagbaju/oder
Optimising Definitions of Expressed Regions
https://github.com/eolagbaju/oder
annotation genomics rna-seq transcriptomics
Last synced: about 1 month ago
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Optimising Definitions of Expressed Regions
- Host: GitHub
- URL: https://github.com/eolagbaju/oder
- Owner: eolagbaju
- Created: 2021-04-13T13:47:50.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2021-10-08T16:13:17.000Z (over 4 years ago)
- Last Synced: 2025-10-20T14:08:16.704Z (5 months ago)
- Topics: annotation, genomics, rna-seq, transcriptomics
- Language: R
- Homepage: https://eolagbaju.github.io/ODER/
- Size: 15 MB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.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%"
)
```
# ODER
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/ODER)
[](https://github.com/eolagbaju/ODER/actions)
[](https://codecov.io/gh/eolagbaju/ODER?branch=master)
The goal of `ODER` is to **O**ptimise the **D**efinition of **E**xpressed **R**egions. `ODER` is a packaged form of the method developed in the Zhang et al. 2020 publication: [Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders](https://www.science.org/doi/10.1126/sciadv.aay8299). For a more detailed explanation of using `ODER`, please see the [vignette](https://eolagbaju.github.io/ODER/articles/ODERflow.html). For more explanation of the methodology behind `ODER`, see the mehtods section of the [original publication](https://www.science.org/doi/10.1126/sciadv.aay8299).
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `ODER` using from [Bioconductor](http://bioconductor.org/) the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("ODER")
```
And the development version from [GitHub](https://github.com/eolagbaju/ODER) with:
```{r 'install_dev', eval = FALSE}
BiocManager::install("eolagbaju/ODER")
```
## Citation
Below is the citation output from using `citation('ODER')` in R. Please
run this yourself to check for any updates on how to cite __ODER__.
```{r 'citation', eval = requireNamespace('ODER')}
message(citation("ODER"), bibtex = TRUE)
```
Please note that the `ODER` 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 `ODER` 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://eolagbaju.github.io/ODER) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
For more details, check the `dev` directory.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.