Phyloseq swMATH ID: 13730 Software Authors: Paul J. McMurdie; Susan Holmes Description: phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. Background: The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Homepage: https://github.com/joey711/phyloseq Source Code: https://github.com/joey711/phyloseq Dependencies: R Related Software: R; ggplot2; GUniFrac; shiny; vegan; multtest; structSSI; DESeq2; Bioconductor; pplacer; Voom; edgeR; pkgdown; metacoder; magrittr; ggtree; microbiome; microViz; doParallel; foreach Cited in: 5 Publications all top 5 Cited by 11 Authors 1 Bacallado, Sergio 1 Bien, Jacob 1 Favaro, Stefano 1 Holmes, Susan P. 1 Martin, Bryan D. 1 Sankaran, Kris 1 Trippa, Lorenzo 1 Willis, Amy D. 1 Witten, Daniela M. 1 Xia, Yinglin 1 Yan, Xiaohan Cited in 5 Serials 1 Journal of the American Statistical Association 1 Journal of Statistical Planning and Inference 1 The Annals of Applied Statistics 1 Journal of Computational and Graphical Statistics 1 ICSA Book Series in Statistics Cited in 3 Fields 5 Statistics (62-XX) 1 Numerical analysis (65-XX) 1 Biology and other natural sciences (92-XX) Citations by Year