rANOMALY
rANOMALY is an R Package integrating AmplicoN wOrkflow for Microbial community AnaLYsis. Here the F1000 reference paper and the poster presenting this workflow.
Installation
You can install the development version of rANOMALY from this repository with:
Linux (highly recommended)
install.packages("devtools")
devtools::install_git("https://forgemia.inra.fr/umrf/ranomaly")
Windows
Require Rtools, git and run same commands as Linux installation.
Tutorial
Visit the rANOMALY wikipage
Ressources
IDTAXA formatted references databases for 16S and ITS are available here.
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 GPL 3.0
Copyright
2021 INRAE