README.md

<!-- README.md is generated from README.Rmd. Please edit that file -->

# rANOMALY

<!-- badges: start -->

<!-- [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) -->

<!-- badges: end -->

rANOMALY is an R Package integrating AmplicoN wOrkflow for Microbial community AnaLYsis. [Here the
F1000 reference paper](https://f1000research.com/articles/10-7) and [the
poster](https://hal.archives-ouvertes.fr/hal-02340484/) presenting this workflow.

## Installation

You can install the development version of rANOMALY from this repository
with:

### Linux (highly recommended)

``` r
install.packages("devtools")
devtools::install_git("https://forgemia.inra.fr/umrf/ranomaly")
```

### Windows

Require [Rtools](https://cran.r-project.org/bin/windows/Rtools/),
[git](https://git-scm.com/download/win) and run same commands as Linux
installation.

## Tutorial

Visit [the rANOMALY
wikipage](https://forgemia.inra.fr/umrf/ranomaly/-/wikis/home)

## Ressources

IDTAXA formatted references databases for 16S and ITS are [available
here](https://nextcloud.inrae.fr/s/YHi3fmDdEJt5cqR).

## Citation

Sebastien Theil and Etienne Rifa. « RANOMALY: AmplicoN WOrkflow for Microbial Community AnaLYsis ». F1000Research 10 (07/01/2021): 7. https://doi.org/10.12688/f1000research.27268.1.

If you use rANOMALY, please cite following tools:

Callahan, Benjamin J., Paul J. McMurdie, Michael J. Rosen, Andrew W. Han, Amy Jo A. Johnson, et Susan P. Holmes. « DADA2: High-Resolution Sample Inference from Illumina Amplicon Data ». Nature Methods 13, nᵒ 7 (juillet 2016): 581‑83. https://doi.org/10.1038/nmeth.3869.

McMurdie, Paul J., et Susan Holmes. « Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data ». PLOS ONE 8, nᵒ 4 (22 avril 2013): e61217. https://doi.org/10.1371/journal.pone.0061217.

Murali, Adithya, Aniruddha Bhargava, et Erik S. Wright. « IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences ». Microbiome 6, nᵒ 1 (9 août 2018): 140. https://doi.org/10.1186/s40168-018-0521-5.

## Licence

 ![etalab](inst/misc/etalab5.png "etalab") [ETALAB](https://www.etalab.gouv.fr/wp-content/uploads/2018/11/open-licence.pdf)
GPL 3.0

## Copyright
2021 INRA