├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── other_issue.md └── workflows │ ├── R-CMD-check.yaml │ ├── draft-pdf.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── .lintr ├── .vscode └── settings.json ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE.md ├── MiscMetabar.Rproj ├── NAMESPACE ├── NEWS.md ├── R ├── Deseq2_edgeR.R ├── MiscMetabar-package.R ├── alpha_div_test.R ├── beta_div_test.R ├── blast.R ├── controls.R ├── dada_phyloseq.R ├── data.R ├── deprecated.R ├── funguild.R ├── krona.R ├── lulu.R ├── miscellanous.R ├── plot_functions.R ├── speedyseq_functions.R ├── table_functions.R ├── targets_misc.R ├── taxonomy.R └── vsearch.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── citation.cff ├── cran-comments.md ├── data ├── Tengeler2020_pq.rda ├── data_fungi.rda ├── data_fungi_mini.rda └── data_fungi_sp_known.rda ├── docs ├── .nojekyll ├── 404.html ├── CODE_OF_CONDUCT.html ├── CONTRIBUTING.html ├── LICENSE.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── MiscMetabar.html │ ├── MiscMetabar_files │ │ ├── crosstalk-1.2.0 │ │ │ ├── css │ │ │ │ └── crosstalk.min.css │ │ │ ├── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ │ └── scss │ │ │ │ └── crosstalk.scss │ │ ├── crosstalk-1.2.1 │ │ │ ├── css │ │ │ │ └── crosstalk.min.css │ │ │ ├── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ │ └── scss │ │ │ │ └── crosstalk.scss │ │ ├── crosstalk-1.2.2 │ │ │ ├── css │ │ │ │ └── crosstalk.min.css │ │ │ ├── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ │ └── scss │ │ │ │ └── crosstalk.scss │ │ ├── d3-4.5.0 │ │ │ ├── LICENSE │ │ │ └── d3.min.js │ │ ├── d3-4.9.1 │ │ │ ├── LICENSE │ │ │ └── d3.min.js │ │ ├── datatables-binding-0.30 │ │ │ └── datatables.js │ │ ├── datatables-binding-0.31 │ │ │ └── datatables.js │ │ ├── datatables-binding-0.32 │ │ │ ├── datatables.js │ │ │ ├── fastqc_data.txt │ │ │ ├── fastqc_report.html │ │ │ └── summary.txt │ │ ├── datatables-binding-0.33 │ │ │ └── datatables.js │ │ ├── datatables-binding-0.34.0 │ │ │ └── datatables.js │ │ ├── datatables-css-0.0.0 │ │ │ └── datatables-crosstalk.css │ │ ├── dt-core-1.13.4 │ │ │ ├── css │ │ │ │ ├── jquery.dataTables.extra.css │ │ │ │ └── jquery.dataTables.min.css │ │ │ └── js │ │ │ │ └── jquery.dataTables.min.js │ │ ├── dt-core-1.13.6 │ │ │ ├── css │ │ │ │ ├── jquery.dataTables.extra.css │ │ │ │ └── jquery.dataTables.min.css │ │ │ └── js │ │ │ │ └── jquery.dataTables.min.js │ │ ├── figure-html │ │ │ ├── example-1.png │ │ │ └── unnamed-chunk-4-1.png │ │ ├── htmltools-fill-0.5.8.1 │ │ │ └── fill.css │ │ ├── htmlwidgets-1.6.2 │ │ │ └── htmlwidgets.js │ │ ├── htmlwidgets-1.6.4 │ │ │ └── htmlwidgets.js │ │ ├── sankey-1 │ │ │ ├── d3-4.9.1 │ │ │ │ ├── LICENSE │ │ │ │ └── d3.min.js │ │ │ └── sankey.js │ │ ├── sankeyNetwork-binding-0.4.1 │ │ │ └── sankeyNetwork.js │ │ └── sankeyNetwork-binding-0.4 │ │ │ └── sankeyNetwork.js │ ├── Reclustering.html │ ├── Reclustering_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-4-2.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-6-2.png │ ├── Rules.html │ ├── alpha-div.html │ ├── alpha-div_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-6-2.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-7-2.png │ ├── articles │ │ ├── Reclustering.html │ │ ├── Rules.html │ │ ├── alpha-div.html │ │ ├── beta-div.html │ │ ├── essai_article.html │ │ ├── explore_data.html │ │ ├── fastq_quality_check.html │ │ ├── filter.html │ │ ├── import_export_track.html │ │ ├── pkgnet-report.html │ │ ├── quality_fastq.html │ │ ├── states_of_fields_in_R.html │ │ ├── tengeler.html │ │ └── tree_visualization.html │ ├── beta-div.html │ ├── beta-div_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-14-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── essai_article.html │ ├── explore_data.html │ ├── explore_data_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-7-1.png │ ├── fastq_quality_check.html │ ├── filter.html │ ├── import_export_track.html │ ├── index.html │ ├── pkgnet-report.html │ ├── pkgnet-report_files │ │ ├── crosstalk-1.2.1 │ │ │ ├── css │ │ │ │ └── crosstalk.min.css │ │ │ ├── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ │ └── scss │ │ │ │ └── crosstalk.scss │ │ ├── crosstalk-1.2.2 │ │ │ ├── css │ │ │ │ └── crosstalk.min.css │ │ │ ├── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ │ └── scss │ │ │ │ └── crosstalk.scss │ │ ├── datatables-binding-0.33 │ │ │ └── datatables.js │ │ ├── datatables-binding-0.34.0 │ │ │ └── datatables.js │ │ ├── datatables-css-0.0.0 │ │ │ └── datatables-crosstalk.css │ │ ├── dt-core-1.13.6 │ │ │ ├── css │ │ │ │ ├── jquery.dataTables.extra.css │ │ │ │ └── jquery.dataTables.min.css │ │ │ └── js │ │ │ │ └── jquery.dataTables.min.js │ │ ├── htmltools-fill-0.5.8.1 │ │ │ └── fill.css │ │ ├── htmlwidgets-1.6.4 │ │ │ └── htmlwidgets.js │ │ ├── vis-9.1.0 │ │ │ ├── add_css.txt │ │ │ ├── img │ │ │ │ └── network │ │ │ │ │ ├── acceptDeleteIcon.png │ │ │ │ │ ├── addNodeIcon.png │ │ │ │ │ ├── backIcon.png │ │ │ │ │ ├── connectIcon.png │ │ │ │ │ ├── cross.png │ │ │ │ │ ├── cross2.png │ │ │ │ │ ├── deleteIcon.png │ │ │ │ │ ├── downArrow.png │ │ │ │ │ ├── editIcon.png │ │ │ │ │ ├── leftArrow.png │ │ │ │ │ ├── minus.png │ │ │ │ │ ├── plus.png │ │ │ │ │ ├── rightArrow.png │ │ │ │ │ ├── upArrow.png │ │ │ │ │ └── zoomExtends.png │ │ │ ├── vis-network.min.css │ │ │ └── vis-network.min.js │ │ ├── visNetwork-binding-2.1.2 │ │ │ └── visNetwork.js │ │ └── visNetwork-binding-2.1.4 │ │ │ └── visNetwork.js │ ├── quality_fastq.html │ ├── states_of_fields_in_R.html │ ├── tengeler.html │ ├── tengeler_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-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── tree_visualization.html │ └── tree_visualization_files │ │ └── figure-html │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-3-2.png │ │ ├── unnamed-chunk-3-3.png │ │ ├── unnamed-chunk-3-4.png │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-4-2.png ├── authors.html ├── deps │ ├── bootstrap-5.2.2 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.4.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── font-awesome-6.5.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── extra.css ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── logo.png ├── news │ └── index.html ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── LCBD_pq.html │ ├── MiscMetabar-deprecated.html │ ├── MiscMetabar-package.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Rplot004.png │ ├── Rplot005.png │ ├── Rplot006.png │ ├── Rplot007.png │ ├── Rplot008.png │ ├── Rplot009.png │ ├── Rplot010.png │ ├── SRS_curve_pq-1.png │ ├── SRS_curve_pq-2.png │ ├── SRS_curve_pq.html │ ├── Tengeler2020_pq.html │ ├── accu_plot-1.png │ ├── accu_plot-2.png │ ├── accu_plot.html │ ├── accu_plot_balanced_modality-1.png │ ├── accu_plot_balanced_modality-2.png │ ├── accu_plot_balanced_modality.html │ ├── accu_samp_threshold-1.png │ ├── accu_samp_threshold.html │ ├── add_blast_info.html │ ├── add_dna_to_phyloseq.html │ ├── add_funguild_info.html │ ├── add_info_to_sam_data-1.png │ ├── add_info_to_sam_data-2.png │ ├── add_info_to_sam_data.html │ ├── add_new_taxonomy_pq.html │ ├── adonis_phyloseq.html │ ├── adonis_pq.html │ ├── adonis_rarperm_pq.html │ ├── all_object_size.html │ ├── ancombc_pq-1.png │ ├── ancombc_pq.html │ ├── are_modality_even_depth-1.png │ ├── are_modality_even_depth.html │ ├── as_binary_otu_table.html │ ├── assign_blastn.html │ ├── assign_dada2.html │ ├── assign_idtaxa.html │ ├── assign_sintax-1.png │ ├── assign_sintax.html │ ├── assign_vsearch_lca.html │ ├── asv2otu.html │ ├── bad_flush_right.html │ ├── bad_or_unique.html │ ├── biplot_physeq.html │ ├── biplot_pq-1.png │ ├── biplot_pq.html │ ├── blast_pq.html │ ├── blast_to_derep.html │ ├── blast_to_phyloseq.html │ ├── build_phytree_pq-1.png │ ├── build_phytree_pq-2.png │ ├── build_phytree_pq-3.png │ ├── build_phytree_pq-4.png │ ├── build_phytree_pq-5.png │ ├── build_phytree_pq-6.png │ ├── build_phytree_pq-7.png │ ├── build_phytree_pq-8.png │ ├── build_phytree_pq.html │ ├── chimera_detection_vs.html │ ├── chimera_removal_vs.html │ ├── circle_pq-1.png │ ├── circle_pq-2.png │ ├── circle_pq-3.png │ ├── circle_pq.html │ ├── clean_physeq.html │ ├── clean_pq.html │ ├── compare_pairs_pq.html │ ├── count_seq.html │ ├── cutadapt_remove_primers.html │ ├── data_fungi.html │ ├── data_fungi_mini.html │ ├── data_fungi_sp_known.html │ ├── diff_fct_diff_class.html │ ├── dist_bycol.html │ ├── dist_pos_control-1.png │ ├── dist_pos_control.html │ ├── distri_1_taxa.html │ ├── fac2col.html │ ├── figures │ │ ├── README-example-1.png │ │ ├── README-unnamed-chunk-2-1.png │ │ ├── README-unnamed-chunk-3-1.png │ │ ├── README-unnamed-chunk-4-1.png │ │ ├── README-unnamed-chunk-5-1.png │ │ ├── README-unnamed-chunk-6-1.png │ │ ├── README-unnamed-chunk-6-2.png │ │ ├── README-unnamed-chunk-6-3.png │ │ ├── README-unnamed-chunk-7-1.png │ │ ├── README-unnamed-chunk-8-1.png │ │ ├── README-unnamed-chunk-8-2.png │ │ ├── lifecycle-archived.svg │ │ ├── lifecycle-defunct.svg │ │ ├── lifecycle-deprecated.svg │ │ ├── lifecycle-experimental.svg │ │ ├── lifecycle-maturing.svg │ │ ├── lifecycle-questioning.svg │ │ ├── lifecycle-stable.svg │ │ ├── lifecycle-superseded.svg │ │ └── logo.png │ ├── filt_taxa_pq.html │ ├── filt_taxa_wo_NA.html │ ├── filter_asv_blast.html │ ├── filter_taxa_blast.html │ ├── filter_trim.html │ ├── format2dada2.html │ ├── format2dada2_species.html │ ├── format2sintax.html │ ├── formattable_pq.html │ ├── funguild_assign.html │ ├── funky_color.html │ ├── get_file_extension.html │ ├── get_funguild_db.html │ ├── ggVenn_phyloseq.html │ ├── ggaluv_pq-1.png │ ├── ggaluv_pq-2.png │ ├── ggaluv_pq.html │ ├── ggbetween_pq-1.png │ ├── ggbetween_pq-2.png │ ├── ggbetween_pq-3.png │ ├── ggbetween_pq.html │ ├── ggscatt_pq-1.png │ ├── ggscatt_pq-2.png │ ├── ggscatt_pq.html │ ├── ggvenn_pq-1.png │ ├── ggvenn_pq-10.png │ ├── ggvenn_pq-2.png │ ├── ggvenn_pq-3.png │ ├── ggvenn_pq-4.png │ ├── ggvenn_pq-5.png │ ├── ggvenn_pq-6.png │ ├── ggvenn_pq-7.png │ ├── ggvenn_pq-8.png │ ├── ggvenn_pq-9.png │ ├── ggvenn_pq.html │ ├── glmutli_pq.html │ ├── graph_test_pq-1.png │ ├── graph_test_pq-2.png │ ├── graph_test_pq.html │ ├── heat_tree_pq-1.png │ ├── heat_tree_pq.html │ ├── hill_curves_pq-1.png │ ├── hill_curves_pq.html │ ├── hill_phyloseq.html │ ├── hill_pq-1.png │ ├── hill_pq-2.png │ ├── hill_pq.html │ ├── hill_test_rarperm_pq.html │ ├── hill_tuckey_phyloseq.html │ ├── hill_tuckey_pq-1.png │ ├── hill_tuckey_pq-2.png │ ├── hill_tuckey_pq.html │ ├── iNEXT_pq.html │ ├── index.html │ ├── install_pkg_needed.html │ ├── is_cutadapt_installed.html │ ├── is_falco_installed.html │ ├── is_krona_installed.html │ ├── is_mumu_installed.html │ ├── is_swarm_installed.html │ ├── is_vsearch_installed.html │ ├── krona.html │ ├── learn_idtaxa.html │ ├── libs │ │ ├── crosstalk-1.2.0 │ │ │ ├── css │ │ │ │ └── crosstalk.min.css │ │ │ ├── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ │ └── scss │ │ │ │ └── crosstalk.scss │ │ ├── crosstalk-1.2.1 │ │ │ ├── css │ │ │ │ └── crosstalk.min.css │ │ │ ├── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ │ └── scss │ │ │ │ └── crosstalk.scss │ │ ├── crosstalk-1.2.2 │ │ │ ├── css │ │ │ │ └── crosstalk.min.css │ │ │ ├── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ │ └── scss │ │ │ │ └── crosstalk.scss │ │ ├── d3-4.5.0 │ │ │ ├── LICENSE │ │ │ └── d3.min.js │ │ ├── d3-4.9.1 │ │ │ ├── LICENSE │ │ │ └── d3.min.js │ │ ├── datatables-binding-0.30 │ │ │ └── datatables.js │ │ ├── datatables-binding-0.31 │ │ │ └── datatables.js │ │ ├── datatables-binding-0.32 │ │ │ ├── datatables.js │ │ │ ├── fastqc_data.txt │ │ │ ├── fastqc_report.html │ │ │ └── summary.txt │ │ ├── datatables-binding-0.33 │ │ │ └── datatables.js │ │ ├── datatables-binding-0.34.0 │ │ │ └── datatables.js │ │ ├── datatables-css-0.0.0 │ │ │ └── datatables-crosstalk.css │ │ ├── dt-core-1.13.4 │ │ │ ├── css │ │ │ │ ├── jquery.dataTables.extra.css │ │ │ │ └── jquery.dataTables.min.css │ │ │ └── js │ │ │ │ └── jquery.dataTables.min.js │ │ ├── dt-core-1.13.6 │ │ │ ├── css │ │ │ │ ├── jquery.dataTables.extra.css │ │ │ │ └── jquery.dataTables.min.css │ │ │ └── js │ │ │ │ └── jquery.dataTables.min.js │ │ ├── htmlwidgets-1.6.2 │ │ │ └── htmlwidgets.js │ │ ├── htmlwidgets-1.6.4 │ │ │ └── htmlwidgets.js │ │ ├── sankey-1 │ │ │ ├── d3-4.9.1 │ │ │ │ ├── LICENSE │ │ │ │ └── d3.min.js │ │ │ └── sankey.js │ │ ├── sankeyNetwork-binding-0.4.1 │ │ │ └── sankeyNetwork.js │ │ └── sankeyNetwork-binding-0.4 │ │ │ └── sankeyNetwork.js │ ├── list_fastq_files.html │ ├── lulu.html │ ├── lulu_phyloseq.html │ ├── lulu_pq.html │ ├── merge_groups.html │ ├── merge_krona.html │ ├── merge_samples2,otu_table-method.html │ ├── merge_samples2,phyloseq-method.html │ ├── merge_samples2,sample_data-method.html │ ├── merge_samples2.html │ ├── merge_taxa_vec,XStringSet-method.html │ ├── merge_taxa_vec,otu_table-method.html │ ├── merge_taxa_vec,phylo-method.html │ ├── merge_taxa_vec,phyloseq-method.html │ ├── merge_taxa_vec,taxonomyTable-method.html │ ├── merge_taxa_vec.html │ ├── merge_taxa_vec_pseudo.html │ ├── multi_biplot_pq-1.png │ ├── multi_biplot_pq-2.png │ ├── multi_biplot_pq-3.png │ ├── multi_biplot_pq-4.png │ ├── multi_biplot_pq-5.png │ ├── multi_biplot_pq-6.png │ ├── multi_biplot_pq.html │ ├── multipatt_pq-1.png │ ├── multipatt_pq-2.png │ ├── multipatt_pq.html │ ├── multiplot.html │ ├── multitax_bar_pq-1.png │ ├── multitax_bar_pq-2.png │ ├── multitax_bar_pq-3.png │ ├── multitax_bar_pq.html │ ├── mumu_pq.html │ ├── no_legend-1.png │ ├── no_legend-2.png │ ├── no_legend.html │ ├── normalize_prop_pq-1.png │ ├── normalize_prop_pq.html │ ├── otu_circle.html │ ├── perc.html │ ├── phyloseq_to_edgeR.html │ ├── physeq_graph_test.html │ ├── physeq_heat_tree.html │ ├── physeq_or_string_to_dna.html │ ├── plot_LCBD_pq-1.png │ ├── plot_LCBD_pq-2.png │ ├── plot_LCBD_pq-3.png │ ├── plot_LCBD_pq-4.png │ ├── plot_LCBD_pq.html │ ├── plot_SCBD_pq-1.png │ ├── plot_SCBD_pq-2.png │ ├── plot_SCBD_pq.html │ ├── plot_ancombc_pq-1.png │ ├── plot_ancombc_pq-2.png │ ├── plot_ancombc_pq-3.png │ ├── plot_ancombc_pq.html │ ├── plot_complexity_pq-1.png │ ├── plot_complexity_pq-2.png │ ├── plot_complexity_pq-3.png │ ├── plot_complexity_pq-4.png │ ├── plot_complexity_pq.html │ ├── plot_deseq2_phyloseq.html │ ├── plot_deseq2_pq-1.png │ ├── plot_deseq2_pq-2.png │ ├── plot_deseq2_pq.html │ ├── plot_edgeR_phyloseq.html │ ├── plot_edgeR_pq-1.png │ ├── plot_edgeR_pq-2.png │ ├── plot_edgeR_pq.html │ ├── plot_guild_pq-1.png │ ├── plot_guild_pq.html │ ├── plot_mt-1.png │ ├── plot_mt-2.png │ ├── plot_mt.html │ ├── plot_refseq_extremity_pq-1.png │ ├── plot_refseq_extremity_pq-2.png │ ├── plot_refseq_extremity_pq-3.png │ ├── plot_refseq_extremity_pq-4.png │ ├── plot_refseq_extremity_pq-5.png │ ├── plot_refseq_extremity_pq-6.png │ ├── plot_refseq_extremity_pq.html │ ├── plot_refseq_pq-1.png │ ├── plot_refseq_pq-2.png │ ├── plot_refseq_pq.html │ ├── plot_seq_ratio_pq-1.png │ ├── plot_seq_ratio_pq-2.png │ ├── plot_seq_ratio_pq-3.png │ ├── plot_seq_ratio_pq.html │ ├── plot_tax_pq-1.png │ ├── plot_tax_pq-2.png │ ├── plot_tax_pq-3.png │ ├── plot_tax_pq.html │ ├── plot_tsne_pq-1.png │ ├── plot_tsne_pq-2.png │ ├── plot_tsne_pq-3.png │ ├── plot_tsne_pq.html │ ├── plot_var_part_pq-1.png │ ├── plot_var_part_pq-2.png │ ├── plot_var_part_pq-3.png │ ├── plot_var_part_pq.html │ ├── postcluster_pq.html │ ├── psmelt_samples_pq-1.png │ ├── psmelt_samples_pq-2.png │ ├── psmelt_samples_pq-3.png │ ├── psmelt_samples_pq-4.png │ ├── psmelt_samples_pq.html │ ├── rarefy_sample_count_by_modality-1.png │ ├── rarefy_sample_count_by_modality.html │ ├── read_phyloseq.html │ ├── read_pq.html │ ├── rename_samples.html │ ├── rename_samples_otu_table.html │ ├── reorder_taxa_pq.html │ ├── resolve_vector_ranks.html │ ├── ridges_pq-1.png │ ├── ridges_pq-2.png │ ├── ridges_pq-3.png │ ├── ridges_pq-4.png │ ├── ridges_pq-5.png │ ├── ridges_pq-6.png │ ├── ridges_pq.html │ ├── rotl_pq-1.png │ ├── rotl_pq-2.png │ ├── rotl_pq.html │ ├── sam_data_matching_names.html │ ├── sample_data_stable.html │ ├── sample_data_with_new_names.html │ ├── sankey_phyloseq.html │ ├── sankey_pq.html │ ├── save_pq.html │ ├── search_exact_seq_pq.html │ ├── select_one_sample.html │ ├── select_taxa,XStringSet,character-method.html │ ├── select_taxa,otu_table,character-method.html │ ├── select_taxa,phylo,character-method.html │ ├── select_taxa,phyloseq,character-method.html │ ├── select_taxa,sample_data,character-method.html │ ├── select_taxa,taxonomyTable,character-method.html │ ├── select_taxa-methods.html │ ├── signif_ancombc.html │ ├── simplify_taxo.html │ ├── subsample_fastq.html │ ├── subset_samples_pq.html │ ├── subset_taxa_pq.html │ ├── subset_taxa_tax_control.html │ ├── summary_plot_phyloseq.html │ ├── summary_plot_pq-1.png │ ├── summary_plot_pq-2.png │ ├── summary_plot_pq-3.png │ ├── summary_plot_pq.html │ ├── swarm_clustering-1.png │ ├── swarm_clustering-2.png │ ├── swarm_clustering.html │ ├── tax_bar_pq-1.png │ ├── tax_bar_pq-2.png │ ├── tax_bar_pq-3.png │ ├── tax_bar_pq-4.png │ ├── tax_bar_pq.html │ ├── tax_datatable.html │ ├── taxa_as_columns.html │ ├── taxa_as_rows.html │ ├── taxa_only_in_one_level.html │ ├── tbl_sum_samdata.html │ ├── tbl_sum_taxtable.html │ ├── track_wkflow.html │ ├── track_wkflow_samples.html │ ├── transp.html │ ├── treemap_pq-1.png │ ├── treemap_pq-2.png │ ├── treemap_pq-3.png │ ├── treemap_pq.html │ ├── tsne_pq.html │ ├── umap_pq-1.png │ ├── umap_pq-2.png │ ├── umap_pq.html │ ├── unique_or_na.html │ ├── upset_pq-1.png │ ├── upset_pq-10.png │ ├── upset_pq-2.png │ ├── upset_pq-3.png │ ├── upset_pq-4.png │ ├── upset_pq-5.png │ ├── upset_pq-6.png │ ├── upset_pq-7.png │ ├── upset_pq-8.png │ ├── upset_pq-9.png │ ├── upset_pq.html │ ├── upset_test_pq.html │ ├── var_par_pq.html │ ├── var_par_rarperm_pq.html │ ├── venn_phyloseq.html │ ├── venn_pq-1.png │ ├── venn_pq-2.png │ ├── venn_pq-3.png │ ├── venn_pq-4.png │ ├── venn_pq-5.png │ ├── venn_pq.html │ ├── verify_pq.html │ ├── vs_search_global.html │ ├── vsearch_clustering-1.png │ ├── vsearch_clustering-2.png │ ├── vsearch_clustering.html │ ├── write_phyloseq.html │ └── write_pq.html ├── search.json └── sitemap.xml ├── inst ├── WORDLIST └── extdata │ ├── 100_sp_UNITE_sh_general_release_dynamic.fasta │ ├── 100_sp_UNITE_sh_general_release_dynamic_dadaSpecies.fasta │ ├── 100_sp_UNITE_sh_general_release_dynamic_sintax.fasta │ ├── dbase.ndb │ ├── dbase.nhr │ ├── dbase.nin │ ├── dbase.not │ ├── dbase.nsq │ ├── dbase.ntf │ ├── dbase.nto │ ├── ex.fasta │ ├── ex.fastq │ ├── ex_R1_001.fasta │ ├── ex_R1_001.fastq.gz │ ├── ex_R1_002.fasta │ ├── ex_R2_001.fastq.gz │ ├── ex_little.fasta │ ├── mini_UNITE_fungi.fasta.gz │ └── sam_data.csv ├── man ├── LCBD_pq.Rd ├── MiscMetabar-deprecated.Rd ├── MiscMetabar-package.Rd ├── SRS_curve_pq.Rd ├── Tengeler2020_pq.Rd ├── accu_plot.Rd ├── accu_plot_balanced_modality.Rd ├── accu_samp_threshold.Rd ├── add_blast_info.Rd ├── add_dna_to_phyloseq.Rd ├── add_funguild_info.Rd ├── add_info_to_sam_data.Rd ├── add_new_taxonomy_pq.Rd ├── adonis_pq.Rd ├── adonis_rarperm_pq.Rd ├── all_object_size.Rd ├── ancombc_pq.Rd ├── are_modality_even_depth.Rd ├── as_binary_otu_table.Rd ├── assign_blastn.Rd ├── assign_dada2.Rd ├── assign_idtaxa.Rd ├── assign_sintax.Rd ├── assign_vsearch_lca.Rd ├── biplot_pq.Rd ├── blast_pq.Rd ├── blast_to_derep.Rd ├── blast_to_phyloseq.Rd ├── build_phytree_pq.Rd ├── chimera_detection_vs.Rd ├── chimera_removal_vs.Rd ├── circle_pq.Rd ├── clean_pq.Rd ├── compare_pairs_pq.Rd ├── count_seq.Rd ├── cutadapt_remove_primers.Rd ├── data_fungi.Rd ├── data_fungi_mini.Rd ├── data_fungi_sp_known.Rd ├── diff_fct_diff_class.Rd ├── dist_bycol.Rd ├── dist_pos_control.Rd ├── distri_1_taxa.Rd ├── fac2col.Rd ├── figures │ ├── README-example-1.png │ ├── README-unnamed-chunk-4-1.png │ ├── README-unnamed-chunk-5-1.png │ ├── README-unnamed-chunk-6-1.png │ ├── README-unnamed-chunk-7-1.png │ └── README-unnamed-chunk-8-1.png ├── filt_taxa_pq.Rd ├── filt_taxa_wo_NA.Rd ├── filter_asv_blast.Rd ├── filter_trim.Rd ├── format2dada2.Rd ├── format2dada2_species.Rd ├── format2sintax.Rd ├── formattable_pq.Rd ├── funguild_assign.Rd ├── funky_color.Rd ├── get_file_extension.Rd ├── get_funguild_db.Rd ├── ggaluv_pq.Rd ├── ggbetween_pq.Rd ├── ggscatt_pq.Rd ├── ggvenn_pq.Rd ├── glmutli_pq.Rd ├── graph_test_pq.Rd ├── hill_curves_pq.Rd ├── hill_pq.Rd ├── hill_test_rarperm_pq.Rd ├── hill_tuckey_pq.Rd ├── iNEXT_pq.Rd ├── is_cutadapt_installed.Rd ├── is_falco_installed.Rd ├── is_krona_installed.Rd ├── is_mumu_installed.Rd ├── is_swarm_installed.Rd ├── is_vsearch_installed.Rd ├── krona.Rd ├── learn_idtaxa.Rd ├── list_fastq_files.Rd ├── lulu.Rd ├── lulu_pq.Rd ├── merge_krona.Rd ├── merge_samples2.Rd ├── merge_taxa_vec.Rd ├── multi_biplot_pq.Rd ├── multipatt_pq.Rd ├── multiplot.Rd ├── multitax_bar_pq.Rd ├── mumu_pq.Rd ├── no_legend.Rd ├── normalize_prop_pq.Rd ├── perc.Rd ├── phyloseq_to_edgeR.Rd ├── physeq_or_string_to_dna.Rd ├── plot_LCBD_pq.Rd ├── plot_SCBD_pq.Rd ├── plot_ancombc_pq.Rd ├── plot_complexity_pq.Rd ├── plot_deseq2_pq.Rd ├── plot_edgeR_pq.Rd ├── plot_guild_pq.Rd ├── plot_mt.Rd ├── plot_refseq_extremity_pq.Rd ├── plot_refseq_pq.Rd ├── plot_seq_ratio_pq.Rd ├── plot_tax_pq.Rd ├── plot_tsne_pq.Rd ├── plot_var_part_pq.Rd ├── postcluster_pq.Rd ├── psmelt_samples_pq.Rd ├── rarefy_sample_count_by_modality.Rd ├── read_pq.Rd ├── rename_samples.Rd ├── rename_samples_otu_table.Rd ├── reorder_taxa_pq.Rd ├── resolve_vector_ranks.Rd ├── ridges_pq.Rd ├── rotl_pq.Rd ├── sam_data_matching_names.Rd ├── sample_data_with_new_names.Rd ├── sankey_pq.Rd ├── save_pq.Rd ├── search_exact_seq_pq.Rd ├── select_one_sample.Rd ├── select_taxa-methods.Rd ├── signif_ancombc.Rd ├── simplify_taxo.Rd ├── subsample_fastq.Rd ├── subset_samples_pq.Rd ├── subset_taxa_pq.Rd ├── subset_taxa_tax_control.Rd ├── summary_plot_pq.Rd ├── swarm_clustering.Rd ├── tax_bar_pq.Rd ├── tax_datatable.Rd ├── taxa_as_columns.Rd ├── taxa_as_rows.Rd ├── taxa_only_in_one_level.Rd ├── tbl_sum_samdata.Rd ├── tbl_sum_taxtable.Rd ├── track_wkflow.Rd ├── track_wkflow_samples.Rd ├── transp.Rd ├── treemap_pq.Rd ├── tsne_pq.Rd ├── umap_pq.Rd ├── unique_or_na.Rd ├── upset_pq.Rd ├── upset_test_pq.Rd ├── var_par_pq.Rd ├── var_par_rarperm_pq.Rd ├── venn_pq.Rd ├── verify_pq.Rd ├── vs_search_global.Rd ├── vsearch_clustering.Rd └── write_pq.Rd ├── paper ├── bibliography.bib ├── figures_svg │ ├── description_MiscMetabar.svg │ ├── table1.svg │ ├── table1_publication.svg │ ├── table_1old.svg │ ├── tengeler_MiscMetabar.svg │ └── tengeler_MiscMetabar_editable.svg ├── paper.bib ├── paper.md ├── paper_old.md ├── table1_publication.svg └── tengeler_MiscMetabar.svg ├── pkgdown ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── spelling.R ├── testthat.R └── testthat │ ├── Rplots.pdf │ ├── inst │ └── extdata │ │ ├── 1000_sp_UNITE_sh_general_release_dynamic.fasta │ │ ├── dbase.ndb │ │ ├── dbase.nhr │ │ ├── dbase.nin │ │ ├── dbase.not │ │ ├── dbase.nsq │ │ ├── dbase.ntf │ │ ├── dbase.nto │ │ ├── ex.fasta │ │ ├── ex.fastq │ │ ├── ex_R1_001.fastq.gz │ │ ├── ex_R2_001.fastq.gz │ │ └── ex_little.fasta │ ├── log.txt │ ├── test_adonis.R │ ├── test_blast.R │ ├── test_clean_pq.R │ ├── test_controls.R │ ├── test_cutadapt.R │ ├── test_deprecated.R │ ├── test_deseq2_edgeR.R │ ├── test_figures_alpha_div.R │ ├── test_figures_beta_div.R │ ├── test_figures_biplot.R │ ├── test_figures_misc.R │ ├── test_figures_summary_plot.R │ ├── test_figures_taxo.R │ ├── test_krona.R │ ├── test_misc.R │ ├── test_phyloseq_class.R │ ├── test_rw.R │ ├── test_subset.R │ ├── test_swarm.R │ ├── test_table_functions.R 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