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README.Rmd
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README.Rmd
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---
output: github_document
bibliography: references/references.bib
csl: references/plos-computational-biology.csl
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = ""
)
```
# Real Data Analysis With coiaf
<!-- badges: start -->
[![DOI](https://zenodo.org/badge/440980542.svg)](https://zenodo.org/badge/latestdoi/440980542)
[![Requirement](https://img.shields.io/badge/requirement-coiaf-green)](https://github.com/bailey-lab/coiaf)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
<!-- badges: end -->
This repository stores the real data analysis conducted to test the software
package [{coiaf}](https://github.com/bailey-lab/coiaf).
## Data Source
We analysed samples from the MalariaGEN *Plasmodium falciparum* Community
Project [@malariagen_open_2021]. The MalariaGEN *Plasmodium falciparum*
Community Project provides genomic data from over 7,000 *P. falciparum* samples
from 28 malaria-endemic countries in Africa, Asia, South America, and Oceania
from 2002-2015. Detailed information about the data release including brief
descriptions of contributing partner studies and study locations is available in
the supplementary of MalariaGEN *et al.*.
## Project Structure
```{r proj structure, echo = FALSE}
fs::dir_tree(
regexp = "renv.*|library|.*-figures|archive|.*Rproj|.*E.R?md|.*html|data-outputs/vary-seq-error/*|references",
invert = TRUE
)
```
## References