├── .Rbuildignore ├── .github ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE.md └── PULL_REQUEST_TEMPLATE.md ├── .gitignore ├── .travis.yml ├── CITATION.cff ├── DESCRIPTION ├── LICENSE ├── MicrobiomeR.Rproj ├── NAMESPACE ├── NEWS.md ├── R ├── MicrobiomeR-package.R ├── alpha-diversity.R ├── barplot.R ├── correlation-plot.R ├── data.R ├── heat-tree.R ├── metacoder-formatting.R ├── metacoder.R ├── ordination.R ├── package.R ├── palettes.R ├── permanova.R ├── phyloseq.R ├── utils-pipe.R └── utils.R ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── data ├── phyloseq_silva_2.rda ├── phyloseq_silva_3.rda ├── raw_silva_2.rda └── raw_silva_3.rda ├── docs ├── CNAME ├── CODE_OF_CONDUCT.html ├── CONTRIBUTING.html ├── ISSUE_TEMPLATE.html ├── LICENSE-text.html ├── PULL_REQUEST_TEMPLATE.html ├── articles │ ├── Microbiome-Workflow.png │ ├── about.html │ ├── about_files │ │ ├── Proj4Leaflet-1.0.1 │ │ │ ├── proj4-compressed.js │ │ │ └── proj4leaflet.js │ │ ├── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ └── unnamed-chunk-1-2.png │ │ ├── htmlwidgets-1.3 │ │ │ └── htmlwidgets.js │ │ ├── jquery-1.12.4 │ │ │ └── jquery.min.js │ │ ├── leaflet-1.3.1 │ │ │ ├── images │ │ │ │ ├── layers-2x.png │ │ │ │ ├── layers.png │ │ │ │ ├── marker-icon-2x.png │ │ │ │ ├── marker-icon.png │ │ │ │ └── marker-shadow.png │ │ │ ├── leaflet.css │ │ │ └── leaflet.js │ │ ├── leaflet-binding-2.0.2 │ │ │ └── leaflet.js │ │ ├── leafletfix-1.0.0 │ │ │ └── leafletfix.css │ │ └── rstudio_leaflet-1.3.1 │ │ │ ├── images │ │ │ └── 1px.png │ │ │ └── rstudio_leaflet.css │ ├── analysis.html │ ├── analysis_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-13-2.png │ │ │ ├── unnamed-chunk-13-3.png │ │ │ ├── unnamed-chunk-13-4.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-7-2.png │ │ │ ├── unnamed-chunk-7-3.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ ├── unnamed-chunk-8-2.png │ │ │ ├── unnamed-chunk-8-3.png │ │ │ ├── unnamed-chunk-9-1.png │ │ │ ├── unnamed-chunk-9-2.png │ │ │ ├── unnamed-chunk-9-3.png │ │ │ ├── unnamed-chunk-9-4.png │ │ │ ├── unnamed-chunk-9-5.png │ │ │ └── unnamed-chunk-9-6.png │ ├── color-palettes.html │ ├── color-palettes_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-1-2.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-2-2.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-3-2.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ └── unnamed-chunk-5-1.png │ ├── data-wrangling.html │ ├── filtering.html │ ├── index.html │ ├── introduction.html │ └── paper.html ├── authors.html ├── docsearch.css ├── docsearch.js ├── extra.css ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── MicrobiomeR.html │ ├── MicrobiomeR_Formats.html │ ├── MicrobiomeR_Workflow.html │ ├── agglomerate_metacoder.html │ ├── agglomerate_taxmap.html │ ├── alpha_diversity_measures.html │ ├── alpha_diversity_plot.html │ ├── as_MicrobiomeR_format.html │ ├── as_analyzed_format.html │ ├── as_basic_format.html │ ├── as_custom_format.html │ ├── as_phyloseq_format.html │ ├── as_raw_format.html │ ├── combination_palette.html │ ├── convert_proportions.html │ ├── correlation_data.html │ ├── correlation_plot.html │ ├── correlation_plots.html │ ├── cov_filter.html │ ├── create_metacoder.html │ ├── create_phyloseq.html │ ├── create_pub_table.html │ ├── create_taxmap.html │ ├── get_alpha_diversity.html │ ├── get_alpha_diversity_measures.html │ ├── get_color_palette.html │ ├── get_correlation_data.html │ ├── get_correlation_plots.html │ ├── get_distance_methods.html │ ├── get_heat_tree_parameters.html │ ├── get_heat_tree_plots.html │ ├── get_output_dir.html │ ├── get_phyloseq_obj.html │ ├── get_plot_limits.html │ ├── get_treatment_matrix.html │ ├── heat_tree_parameters.html │ ├── heat_tree_plots.html │ ├── index.html │ ├── is_analyzed_format.html │ ├── is_basic_format.html │ ├── is_phyloseq_format.html │ ├── is_raw_format.html │ ├── melt_metacoder.html │ ├── melt_taxmap.html │ ├── metacoder_comp_func_1.html │ ├── mkdir.html │ ├── object_handler.html │ ├── order_metacoder_data.html │ ├── ordination_plot.html │ ├── ordination_plots.html │ ├── otu_id_filter.html │ ├── otu_prevalence_filter.html │ ├── otu_proportion_filter.html │ ├── otutax_to_dataframe.html │ ├── output_dir.html │ ├── parse_taxonomy_greengenes2.html │ ├── parse_taxonomy_silva.html │ ├── parse_taxonomy_silva_128.html │ ├── permanova.html │ ├── phyloseq_greengenes.html │ ├── phyloseq_silva.html │ ├── phyloseq_silva_2.html │ ├── phyloseq_silva_3.html │ ├── phyloseq_to_tibble.html │ ├── pick_new_outgroup.html │ ├── pipe.html │ ├── plot_limits.html │ ├── preprocess_phyloseq.html │ ├── raw_greengenes.html │ ├── raw_silva.html │ ├── raw_silva_2.html │ ├── raw_silva_3.html │ ├── remove_ambiguous_taxa.html │ ├── root_by_longest_edge.html │ ├── root_phyloseq_tree.html │ ├── sample_id_filter.html │ ├── save_alpha_diversity_plots.html │ ├── save_barplot.html │ ├── save_correlation_plots.html │ ├── save_heat_tree_plots.html │ ├── save_ordination_plots.html │ ├── save_stacked_barplot.html │ ├── save_stacked_barplots.html │ ├── save_top_coefficients_barplot.html │ ├── scico_palette.html │ ├── stacked_barplot.html │ ├── stacked_barplots.html │ ├── taxa_prevalence_filter.html │ ├── taxon_id_filter.html │ ├── top_coefficients_barplot.html │ ├── transform_metacoder.html │ ├── transformer.html │ ├── transposer.html │ ├── treatment_matrix.html │ ├── validate_MicrobiomeR_format.html │ ├── viridis_magma_palette.html │ ├── viridis_palette.html │ ├── vlookup.html │ └── which_format.html └── sitemap.xml ├── inst ├── extdata │ ├── greengenes.tre │ ├── greengenes_OTU.biom │ ├── nephele_metadata2.txt │ ├── nephele_metadata3.txt │ ├── process_list.yml │ ├── silva.tre │ └── silva_OTU.biom └── paper │ ├── Microbiome-Workflow.png │ ├── paper.bib │ └── paper.md ├── man ├── MicrobiomeR.Rd ├── MicrobiomeR_Formats.Rd ├── MicrobiomeR_Workflow.Rd ├── agglomerate_taxmap.Rd ├── alpha_diversity_measures.Rd ├── alpha_diversity_plot.Rd ├── as_MicrobiomeR_format.Rd ├── as_analyzed_format.Rd ├── as_basic_format.Rd ├── as_custom_format.Rd ├── as_phyloseq_format.Rd ├── as_raw_format.Rd ├── combination_palette.Rd ├── convert_proportions.Rd ├── correlation_data.Rd ├── correlation_plot.Rd ├── correlation_plots.Rd ├── cov_filter.Rd ├── create_phyloseq.Rd ├── create_pub_table.Rd ├── create_taxmap.Rd ├── figures │ └── logo.png ├── get_color_palette.Rd ├── heat_tree_parameters.Rd ├── heat_tree_plots.Rd ├── is_analyzed_format.Rd ├── is_basic_format.Rd ├── is_phyloseq_format.Rd ├── is_raw_format.Rd ├── melt_taxmap.Rd ├── metacoder_comp_func_1.Rd ├── order_metacoder_data.Rd ├── ordination_plot.Rd ├── ordination_plots.Rd ├── otu_id_filter.Rd ├── otu_prevalence_filter.Rd ├── otu_proportion_filter.Rd ├── output_dir.Rd ├── parse_taxonomy_silva_128.Rd ├── permanova.Rd ├── phyloseq_silva_2.Rd ├── phyloseq_silva_3.Rd ├── pick_new_outgroup.Rd ├── pipe.Rd ├── plot_limits.Rd ├── raw_silva_2.Rd ├── raw_silva_3.Rd ├── root_by_longest_edge.Rd ├── root_phyloseq_tree.Rd ├── sample_id_filter.Rd ├── save_alpha_diversity_plots.Rd ├── save_correlation_plots.Rd ├── save_heat_tree_plots.Rd ├── save_ordination_plots.Rd ├── save_stacked_barplots.Rd ├── save_top_coefficients_barplot.Rd ├── scico_palette.Rd ├── stacked_barplot.Rd ├── stacked_barplots.Rd ├── taxa_prevalence_filter.Rd ├── taxon_id_filter.Rd ├── top_coefficients_barplot.Rd ├── transformer.Rd ├── transposer.Rd ├── treatment_matrix.Rd ├── validate_MicrobiomeR_format.Rd ├── viridis_magma_palette.Rd ├── viridis_palette.Rd ├── vlookup.Rd └── which_format.Rd ├── pkgdown ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests 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