README.Rmd

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# metaPR2 <img src="https://github.com/pr2database/metapr2-shiny/blob/main/inst/img/metapr2_logo.png?raw=true" align="right" />

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## A database of 18S rRNA metabarcodes

**Version**:  2.1.0 - 59 datasets

**Release date**: 2023-05-16

### Presentation

MetaPR2 is a database of published 18S rRNA metabarcodes that have been reprocessed and assigned using PR2. 


### Acessing the database

Access to the database to map, search and download the barcodes can be done in three different ways:

- Using a [web interface](http://shiny.metapr2.org).

- Download the R package and launch the shiny application.

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3 - Download and run a Docker container 
 -->
 
#### 1 - Web interface

* Launch in your browser: http://shiny.metapr2.org
* Help : https://pr2database.github.io/metapr2-shiny/articles/

#### 2 - metaPR2 shiny R package


##### Install the package from GitHub

```{r, eval=FALSE, echo=TRUE}
install.packages(devtools)

devtools::install_github("pr2database/metapr2-shiny")

```

Note: You may have to install some packages required by metapr2 if they are not installed on your machine

##### Alternatively install from [R-universe](https://pr2database.r-universe.dev/ui#packages)
No need in this case to install package `devtools`

```{r, eval=FALSE, echo=TRUE}
# Enable repository from pr2database
options(repos = c(
  pr2database = 'https://pr2database.r-universe.dev',
  CRAN = 'https://cloud.r-project.org'))

# Download and install metapr2 in R
install.packages('metapr2')
```

##### Launch shiny interface with function run_app()

```{r, eval=FALSE, echo=TRUE}
metapr2::run_app()
```

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#### 3 - metaPR2 Docker container

Available from Docker repository: https://hub.docker.com/repository/docker/vaulot/metapr2

* Install docker on your computer: https://docs.docker.com/desktop/

* At shell prompt (can be Linux or Windows Powershell)

```{bash}
# Download container
docker pull vaulot/metapr2:v1.0.2

# Launch container
docker run --rm -p 8080:8080 metapr2

```

* In your browser: http://localhost:8080/
 
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### Help

Extensive help is provided [here](https://pr2database.github.io/metapr2-shiny/articles/).


### Errors

Please report errors in the [Issues page of the metaPR2 database](https://github.com/pr2database/metapr2-shiny/issues).


### Citation

Vaulot, D., Sim, C.W.H., Ong, D., Teo, B., Biwer, C., Jamy, M., Lopes dos Santos, A., 2022. metaPR$^{2}$: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Molecular Ecology Resources 22, 3188–3201. https://doi.org/10.1111/1755-0998.13674



### Resources

* Website: https://shiny.metapr2.org/

* Source code: https://github.com/pr2database/metapr2-shiny

* Docker (only version <= 1.0.2): https://hub.docker.com/repository/docker/vaulot/metapr2

 




### Maintainer
* Daniel Vaulot: vaulot@gmail.com

### Contributors
* Daniel Vaulot, CNRS Roscoff, NTU-ASE Geek lab
* Adriana Lopes dos Santos, NTU-ASE Geek lab 
* Clarence Sim, NTU-ASE Geek lab 
* Denise Ong, NTU-ASE Geek lab 
* Bryan Teo, NTU-ASE Geek lab
* Charlie Biwer, Uppsala University Sweden
* Mahwash Jamy, Uppsala University Sweden