Schuyler D. Smith
phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects
Iowa State University
paper presents phylosmith rpackage enables reproducible efficient analysis microbiome data phyloseqclass objects providing robust efficient functionsphylosmith utilizes standardized data format phyloseq r object accession methods provide functions simple intuitive input argumentsthe functions provided phylosmith divided 3 categories data wranglingthese functions include operations either return transformed version input phyloseq object subset version extracted data set parametersin cases functions practical rewrites ones already available phyloseq additional features efficient implementation datatable large datasetsvarious functions include finding shared exclusive taxa treatments agglomeration factor handling filtering