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##Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies

Files and codes used for analysis of data reported in the review Sudarshan A. Shetty, Floor Hugenholtz, Leo Lahti, Hauke Smidt, Willem M. de Vos; Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiol Rev 2017 fuw045. doi: 10.1093/femsre/fuw045

https://academic.oup.com/femsre/article/doi/10.1093/femsre/fuw045/2979411/Intestinal-microbiome-landscaping-insight-in

https://microsud.github.io/Intestinal-Microbiome-Western-Adults/

You can find step-wise information in the *.Rmd file

###Reference:

Metagenome based Genus compositions:

Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J.R., Prifti, E., Nielsen, T. and Juncker, A.S., 2014. An integrated catalog of reference genes in the human gut microbiome. Nature biotechnology, 32(8), pp.834-841.

Microbiome package: https://github.com/microbiome/microbiome

HITChip profiling data from http://www.nature.com/articles/ncomms5344 by Lahti et al., 2014

qgraph pacakge : http://sachaepskamp.com/qgraph

Phyloseq: https://joey711.github.io/phyloseq/