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https://github.com/avallecam/elixr-casestudy01
https://github.com/avallecam/elixr-casestudy01
Last synced: 1 day ago
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- Host: GitHub
- URL: https://github.com/avallecam/elixr-casestudy01
- Owner: avallecam
- License: gpl-3.0
- Created: 2023-10-03T18:48:43.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2023-10-15T21:16:51.000Z (about 1 year ago)
- Last Synced: 2023-10-16T19:14:17.729Z (about 1 year ago)
- Language: R
- Size: 5.03 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.Rmd
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# elixr-casestudy01
The goal of `elixr-casestudy01` is to host the code used for a serological survey workflow to:
- __Collect__ multiple plate files in a single file using `{plater}`,
- __Standardize__ Antibody Units across multiple plates using method proposed by [Miura K, 2008](https://www.sciencedirect.com/science/article/pii/S0264410X07012601), and
- __Classify__ the seropositivity of the Antibody Units of the sample using method proposed by [Sepulveda N, 2015](https://www.hindawi.com/journals/jir/2015/738030/)
## Installation
* Clone this repository. Follow [this steps to create a new Rstudio Project from a GitHub repository](https://www.epirhandbook.com/en/version-control-and-collaboration-with-git-and-github.html?q=clone#clone-from-a-github-repository).
* Restore the dependencies of this R project, with specific packages and versions, with `renv::restore()`.
* Run:
```{r eval = FALSE}
source("make.R")
```
## Contributing
See our [Contributing guide](/.github/CONTRIBUTING.md) for ways to get started.
Please adhere to this project's [Code of Conduct](/.github/CODE_OF_CONDUCT.md).
## Support
Please see our [Getting help guide](/.github/SUPPORT.md) for support.
## License
[GPLv3](https://choosealicense.com/licenses/gpl-3.0/)
## Authors
- [@avallecam](https://www.github.com/avallecam)
## Acknowledgements
Many thanks for the opportunity to work on this project to the team at:
Laboratorio de Biología Molecular e Inmunología,
Unidad Especializada de Investigación en Productos Naturales Antiparasitarios de la Amazonia,
Centro de Investigación en Recursos Naturales ([CIRNA](https://www.gob.pe/37761-universidad-nacional-de-la-amazonia-peruana-centro-de-investigaciones-de-recursos-naturales-de-la-unap-cirna-unap)),
Universidad Nacional de la Amazonia Peruana ([UNAP](https://enlinea.unapiquitos.edu.pe/)),
Iquitos - Perú.
## References
Miura K, Orcutt AC, Muratova OV, Miller LH, Saul A, Long CA. Development and characterization of a standardized ELISA including a reference serum on each plate to detect antibodies induced by experimental malaria vaccines. Vaccine. 2008;26(2):193-200. doi: [10.1016/j.vaccine.2007.10.064](https://www.sciencedirect.com/science/article/pii/S0264410X07012601).
Sepúlveda N, Stresman G, White MT, Drakeley CJ. Current mathematical models for analyzing anti-malarial antibody data with an eye to malaria elimination and eradication. Journal of Immunology Research. 2015;2015:1-21. doi: [10.1155/2015/738030](https://www.hindawi.com/journals/jir/2015/738030/).
Saavedra-Langer, R., Marapara, J., Valle-Campos, A., Durand, S., Vásquez-Chasnamote, M. E., Silva, H., & Pinedo-Cancino, V. (2018). IgG subclass responses to excreted-secreted antigens of Plasmodium falciparum in a low-transmission malaria area of the Peruvian Amazon. Malaria journal, 17(1), 1-10. doi: [10.1186/s12936-018-2471-6](https://malariajournal.biomedcentral.com/articles/10.1186/s12936-018-2471-6).