GitHub - microbiome/tutorials: Tutorials (original) (raw)

microbiome R package

Tools for the exploration and analysis of microbiome profiling data, with a focus on large-scale population studies and 16S taxonomic profiling. This package extends the genericphyloseq framework for R based microbiome analysis. Your feedback, suggestions and bug reports are welcome.

Installation and use

See the package tutorial.

Contribute

Contributions are very welcome:

• Issue Tracker
• Pull requests
• Subscribe to the mailing list(microbiome-devel@googlegroups.com)
• Star us on the Github page

Publications using the microbiome package

Kindly cite this work as follows: "Leo Lahti et al.(2017). Tools for microbiome analysis in R. Microbiome package version 1.6.0. URL:http://microbiome.github.com/microbiome, and the relevant references listed in the manual page of each function. The list of publications is not exhaustive. Let us know if you know of further publications using the microbiome package; we are collecting these on the website.

Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies. Shetty S, Hugenholtz F, Lahti L, Smidt H, de Vos WM, Danchin A. FEMS Microbiology Reviews fuw045, 2017.

Metagenomics meets time series analysis: unraveling microbial community dynamics Faust K, Lahti L, Gonze D, de Vos WM, Raes J. Current Opinion in Microbiology 15:56-66 2015.

Tipping elements in the human intestinal ecosystemLahti L, Salojärvi J, Salonen A, Scheffer M, de Vos WM. Nature Communications 5:4344, 2014.

Fat, Fiber and Cancer Risk in African, Americans and Rural AfricansO’Keefe S, Li JV, Lahti L, Ou J, Carbonero F, Mohammed K, Posma JM, Kinross J, Wahl E, Ruder E, Vipperla K, Naidoo V, Mtshali L, Tims S, Puylaert PGB, DeLany J, Krasinskas A, Benefiel AC, Kaseb HO, Newton K, Nicholson JK, de Vos WM, Gaskins HR, Zoetendal EG. Nature Communications 6:6342, 2015.

Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling dataLahti L, Salonen A, Kekkonen RA, Salojärvi J, Jalanka-Tuovinen J, Palva A, Orešič M, de Vos WM. PeerJ 1:e32, 2013.

The adult intestinal core microbiota is determined by analysis depth and health statusSalonen A, Salojärvi J, Lahti L, and de Vos WM. Clinical Microbiology and Infection 18(S4):16 20, 2012.

Acknowledgements

Main developer: Leo Lahti

Co-authors: Jarkko Salojärvi, Sudarshan Shetty.

Contributors: Tineka Blake and other contributors to microbiome R package & microbiome tutorial.

Financial support has been provided by the following bodies:

• Academy of Finland (grants 256950 and 295741)
• University of Turku, Department of Mathematics and Statistics
• VIB lab for Bioinformatics and (eco-)systems biology, VIB/KULeuven, Belgium
• Molecular Ecology group, Laboratory of Microbiology, Wageningen University, Netherlands
• Department of Veterinary Bioscience, University of Helsinki, Finland.

This work relies on the independentphyloseq package and data structures for R-based microbiome analysis developed by Paul McMurdie and Susan Holmes.