README.Rmd

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microbiome R package
==========

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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 generic
[phyloseq](https://github.com/joey711/phyloseq) framework for R based
microbiome analysis.  Your feedback, suggestions and bug reports are
welcome.


### Installation and use

See the package [tutorial](http://microbiome.github.io/tutorials/).


### Contribute

Contributions are very welcome:

  * [Issue Tracker](https://github.com/microbiome/microbiome/issues) 
  * [Pull requests](https://github.com/microbiome/microbiome/)
  * Subscribe to the [mailing list](https://groups.google.com/forum/#!forum/microbiome-devel) (microbiome-devel@googlegroups.com)
  * [Star us on the Github page](https://github.com/microbiome/microbiome)


### Publications using the microbiome package

**Kindly cite this work** as follows: "Leo Lahti [et al.](https://github.com/microbiome/microbiome/graphs/contributors) (2017). Tools for microbiome analysis in R. Microbiome package version `r sessionInfo()$otherPkgs$microbiome$Version`. URL: [http://microbiome.github.com/microbiome](https://microbiome.github.io/tutorials), 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](https://academic.oup.com/femsre/article/doi/10.1093/femsre/fuw045/2979411/Intestinal-microbiome-landscaping-insight-in#58802539). 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](http://dx.doi.org/10.1016/j.mib.2015.04.004) 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 ecosystem](http://www.nature.com/ncomms/2014/140708/ncomms5344/full/ncomms5344.html) Lahti 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 Africans](http://www.nature.com/ncomms/2015/150428/ncomms7342/full/ncomms7342.html)  O’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 data](http://dx.doi.org/10.7717/peerj.32) Lahti 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 status](http://onlinelibrary.wiley.com/doi/10.1111/j.1469-0691.2012.03855.x/abstract) Salonen A, Salojärvi J, Lahti L, and de Vos WM. _Clinical Microbiology and Infection_ 18(S4):16 20, 2012. 


### Acknowledgements

Main developer: [Leo Lahti](https://github.com/antagomir/)

Co-authors: Jarkko Salojärvi, Sudarshan Shetty. 

Contributors: Tineka Blake and [other contributors to microbiome R package](https://github.com/microbiome/microbiome/graphs/contributors) [& microbiome tutorial](https://github.com/microbiome/tutorials/graphs/contributors).

Financial support has been provided by the following bodies:

  * Academy of Finland (grants 256950 and 295741)
  * [University of Turku](http://www.utu.fi/en/Pages/home.aspx), Department of Mathematics and Statistics
  * [VIB lab for Bioinformatics and (eco-)systems biology](http://www.vib.be/en/research/scientists/Pages/Jeroen-Raes-Lab.aspx), VIB/KULeuven, Belgium
  * [Molecular Ecology group](http://www.mib.wur.nl/UK/), Laboratory of Microbiology, Wageningen University, Netherlands
  * [Department of Veterinary Bioscience](http://www.vetmed.helsinki.fi/apalva/index.htm), University of Helsinki, Finland.

This work relies on the independent [phyloseq](https://github.com/joey711/phyloseq) package and data structures for R-based microbiome analysis developed by Paul McMurdie and Susan Holmes.