Paul J. McMurdie|Susan Holmes
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Stanford University|Stanford University
analysis microbial communities dna sequencing brings many challenges integration different types data methods ecology genetics phylogenetics multivariate statistics visualization testing increased breadth experimental designs pursued projectspecific statistical analyses often needed analyses often difficult impossible peer researchers independently reproduce vast majority requisite tools performing analyses reproducibly already implemented r extensions packages limited support high throughput microbiome census datahere describe software project phyloseq dedicated objectoriented representation analysis microbiome census data r supports importing data variety common formats well many analysis techniques include calibration filtering subsetting agglomeration multitable comparisons diversity analysis parallelized fast unifrac ordination methods production publicationquality graphics manner easy document share modify show apply functions r packages phyloseqrepresented data illustrating availability large number open source analysis techniques discuss use phyloseq tools reproducible research practice common fields still rare analysis highly parallel microbiome census data made available materials necessary completely reproduce analysis figures included article example best practices reproducible researchthe phyloseq project r new opensource software package freely available web github bioconductor