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; Bioconductor; DESeq2; vegan; structSSI; Voom; edgeR; DADA2; microViz; shiny; GUniFrac; multtest; limma; DEseq; gcrma; pplacer; mia; targets; mumu
Cited in: 7 Documents

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