论文信息 - Using RDPTools Output with Phyloseq

Using RDPTools Output with Phyloseq

You may install R from the Comprehensive R Archive Network (CRAN) repository at http://cran.us. r-project.org/. As an aid to working with R, we suggest that you also install RStudio, an IDE interface for R, available at http://www.rstudio.com/. By loading the Rmd file included with the tutorial files (see below) into RStudio, you can easily recreate the R portions of these tutorials on your own computer. And you can get an explanation of how to use any function in a code block by placing the cursor anywhere in the function name and pressing key F1.

Qiong Wang | John F. Quensen

[1] James R. Cole,et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis , 2013, Nucleic Acids Res..

[2] P. Legendre,et al. vegan : Community Ecology Package. R package version 1.8-5 , 2007 .

[3] J. Tiedje,et al. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[4] Klaus Peter Schliep,et al. phangorn: phylogenetic analysis in R , 2010, Bioinform..

[5] Hongzhe Li,et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances , 2012, Bioinform..

[6] Susan P. Holmes,et al. phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data , 2011, Pacific Symposium on Biocomputing.