R scripts used for analysis of data reported in the review
This project is maintained by microsud
Files and codes used for analysis of data reported in the review by Shetty et al. 2016.
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/