rANOMALY is an R Package integrating AmplicoN wOrkflow for Microbial community AnaLYsis. Here the F1000 reference paper and the poster presenting this workflow.
A shiny app ExploreMetabar is available to explore phyloseq object generated with rANOMALY or other tools, and allow users to perform statistical analysis in an user friendly interface (no command line).
You can install the development version of rANOMALY from this repository with:
install.packages("devtools")
devtools::install_git("https://forgemia.inra.fr/umrf/ranomaly")Require Rtools, git and run same commands as Linux installation.
Visit the rANOMALY wikipage
IDTAXA formatted references databases for 16S and ITS are available here.
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.
ETALAB
GPL 3.0
2021 INRAE