Files in phyloseq

Handling and analysis of high-throughput microbiome census data

README.md R/as-methods.R R/phylo-class.R R/network-methods.R R/allClasses.R R/extend_vegan.R R/extract-methods.R R/allData.R R/otuTable-class.R R/assignment-methods.R R/show-methods.R R/transform_filter-methods.R R/ordination-methods.R R/merge-methods.R R/extend_DESeq2.R R/deprecated_functions.R R/multtest-wrapper.R R/taxonomyTable-class.R R/almostAllAccessors.R R/extend_metagenomeSeq.R R/plot-methods.R R/allPackage.R R/validity-methods.R R/sampleData-class.R R/IO-methods.R R/phyloseq-class.R R/distance-methods.R vignettes/phyloseq-FAQ.Rmd vignettes/phyloseq-analysis.Rmd vignettes/phyloseq-mixture-models.Rmd vignettes/phyloseq-basics.Rmd man/intersect_taxa.Rd man/show-methods.Rd man/threshrank.Rd man/subset_taxa-methods.Rd man/import_mothur_groups.Rd man/sample_variables.Rd man/assign-taxa_names.Rd man/prune_samples-methods.Rd man/import_uparse.Rd man/tip_glom.Rd man/transpose-methods.Rd man/merge_samples-methods.Rd man/assign-sample_data.Rd man/import_RDP_otu.Rd man/gapstat_ord.Rd man/threshrankfun.Rd man/transformcounts.Rd man/merge_phyloseq_pair-methods.Rd man/ordinate.Rd man/get.component.classes.Rd man/plot_clusgap.Rd man/get_taxa_unique.Rd man/import_mothur_otu_table.Rd man/filter_taxa.Rd man/cca-rda-phyloseq-methods.Rd man/get_sample-methods.Rd man/tree_layout.Rd man/phyloseq_to_deseq2.Rd man/sample_names-methods.Rd man/show_mothur_cutoffs.Rd man/nodeplotdefault.Rd man/export_env_file.Rd man/data-GlobalPatterns.Rd man/tax_glom.Rd man/DPCoA.Rd man/topk.Rd man/prune_taxa-methods.Rd man/sample_sums.Rd man/plot_heatmap.Rd man/data-esophagus.Rd man/import_qiime.Rd man/phylo-class.Rd man/rank_names.Rd man/access.Rd man/import_mothur_dist.Rd man/sample_data-class.Rd man/parseTaxonomy-functions.Rd man/filterfun_sample.Rd man/assign-taxa_are_rows.Rd man/read_tree_greengenes.Rd man/envHash2otu_table.Rd man/rarefy_even_depth.Rd man/import_mothur_constaxonomy.Rd man/plot_richness.Rd man/assign-phy_tree.Rd man/phylo.Rd man/taxonomyTable-class.Rd man/merge_phyloseq.Rd man/phyloseq.Rd man/import_qiime_sample_data.Rd man/distance.Rd man/import_env_file.Rd man/dist-class.Rd man/import_RDP_cluster.Rd man/tax_table-methods.Rd man/capscale-phyloseq-methods.Rd man/nodeplotboot.Rd man/subset_samples-methods.Rd man/sample_data-methods.Rd man/plot_bar.Rd man/plot_phyloseq-methods.Rd man/index_reorder.Rd man/phyloseq-class.Rd man/phyloseq-deprecated.Rd man/JSD.Rd man/import_qiime_otu_tax.Rd man/merge_taxa-methods.Rd man/otu_table-methods.Rd man/assign-otu_table.Rd man/metaMDS.Rd man/nodeplotblank.Rd man/export_mothur_dist.Rd man/import_mothur_shared.Rd man/fix_phylo.Rd man/taxa_names-methods.Rd man/phyloseq_to_metagenomeSeq.Rd man/subset_ord_plot.Rd man/import_biom.Rd man/reconcile_categories.Rd man/plot_tree.Rd man/phy_tree-methods.Rd man/rm_outlierf.Rd man/build_tax_table.Rd man/read_tree.Rd man/decorana.Rd man/import_usearch_uc.Rd man/import.Rd man/plot_net.Rd man/import_mothur.Rd man/import_mothur_otulist.Rd man/import_pyrotagger_tab.Rd man/psmelt.Rd man/assign-tax_table.Rd man/pcoa.Rd man/chunkReOrder.Rd man/refseq-methods.Rd man/plot_network.Rd man/otu_table-class.Rd man/ntaxa-methods.Rd man/data-soilrep.Rd man/estimate_richness.Rd man/taxa_sums.Rd man/assign-sample_names.Rd man/get_taxa-methods.Rd man/phyloseq-package.Rd man/extract-methods.Rd man/nsamples-methods.Rd man/distanceMethodList.Rd man/mt-methods.Rd man/data-enterotype.Rd man/splat.phyloseq.objects.Rd man/make_network.Rd man/plot_ordination.Rd man/taxa_are_rows-methods.Rd man/getslots.phyloseq.Rd man/microbio_me_qiime.Rd man/topp.Rd man/get_variable.Rd man/topf.Rd man/plot_scree.Rd man/UniFrac-methods.Rd man/genefilter_sample-methods.Rd tests/testthat-phyloseq.R tests/testthat/test-distance.R tests/testthat/test-rarefy.R tests/testthat/test-merge.R tests/testthat/test-transform.R tests/testthat/test-subset.R tests/testthat/test-plot.R tests/testthat/test-phyloseq.R tests/testthat/test-IO.R inst/doc/phyloseq-FAQ.R inst/doc/phyloseq-analysis.R inst/doc/phyloseq-mixture-models.R inst/doc/phyloseq-basics.R inst/doc/phyloseq-FAQ.Rmd inst/doc/phyloseq-analysis.Rmd inst/doc/phyloseq-mixture-models.Rmd inst/doc/phyloseq-basics.Rmd inst/scripts/installer.R