Files in adrientaudiere/MiscMetabar
Miscellaneous Functions for Metabarcoding Analysis

.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md .github/ISSUE_TEMPLATE/other_issue.md
.github/workflows/R-CMD-check.yaml
.github/workflows/draft-pdf.yaml
.github/workflows/pkgdown.yaml
.github/workflows/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 R/MiscMetabar-package.R R/alpha_div_test.R R/beta_div_test.R R/blast.R R/controls.R R/dada_phyloseq.R R/data.R R/deprecated.R R/funguild.R R/krona.R R/lulu.R R/miscellanous.R R/plot_functions.R R/speedyseq_functions.R R/table_functions.R R/targets_misc.R R/vsearch.R README.Rmd README.md
_pkgdown.yml
citation.cff
cran-comments.md
data/Tengeler2020_pq.rda
data/data_fungi.rda
data/data_fungi_mini.rda
data/data_fungi_sp_known.rda
docs/.nojekyll
docs/404.html
docs/CODE_OF_CONDUCT.html
docs/CONTRIBUTING.html
docs/LICENSE.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/MiscMetabar.html
docs/articles/MiscMetabar_files/crosstalk-1.2.0/css/crosstalk.min.css
docs/articles/MiscMetabar_files/crosstalk-1.2.0/js/crosstalk.js
docs/articles/MiscMetabar_files/crosstalk-1.2.0/js/crosstalk.js.map
docs/articles/MiscMetabar_files/crosstalk-1.2.0/js/crosstalk.min.js
docs/articles/MiscMetabar_files/crosstalk-1.2.0/js/crosstalk.min.js.map
docs/articles/MiscMetabar_files/crosstalk-1.2.0/scss/crosstalk.scss
docs/articles/MiscMetabar_files/crosstalk-1.2.1/css/crosstalk.min.css
docs/articles/MiscMetabar_files/crosstalk-1.2.1/js/crosstalk.js
docs/articles/MiscMetabar_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/articles/MiscMetabar_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/articles/MiscMetabar_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/articles/MiscMetabar_files/crosstalk-1.2.1/scss/crosstalk.scss
docs/articles/MiscMetabar_files/d3-4.5.0/LICENSE
docs/articles/MiscMetabar_files/d3-4.5.0/d3.min.js
docs/articles/MiscMetabar_files/datatables-binding-0.30/datatables.js
docs/articles/MiscMetabar_files/datatables-binding-0.31/datatables.js
docs/articles/MiscMetabar_files/datatables-binding-0.32/datatables.js
docs/articles/MiscMetabar_files/datatables-binding-0.32/fastqc_data.txt
docs/articles/MiscMetabar_files/datatables-binding-0.32/fastqc_report.html
docs/articles/MiscMetabar_files/datatables-binding-0.32/summary.txt
docs/articles/MiscMetabar_files/datatables-binding-0.33/datatables.js
docs/articles/MiscMetabar_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/MiscMetabar_files/dt-core-1.13.4/css/jquery.dataTables.extra.css
docs/articles/MiscMetabar_files/dt-core-1.13.4/css/jquery.dataTables.min.css
docs/articles/MiscMetabar_files/dt-core-1.13.4/js/jquery.dataTables.min.js
docs/articles/MiscMetabar_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
docs/articles/MiscMetabar_files/dt-core-1.13.6/css/jquery.dataTables.min.css
docs/articles/MiscMetabar_files/dt-core-1.13.6/js/jquery.dataTables.min.js
docs/articles/MiscMetabar_files/figure-html/example-1.png
docs/articles/MiscMetabar_files/figure-html/unnamed-chunk-4-1.png
docs/articles/MiscMetabar_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/MiscMetabar_files/htmlwidgets-1.6.2/htmlwidgets.js
docs/articles/MiscMetabar_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/MiscMetabar_files/sankey-1/d3-4.5.0/LICENSE
docs/articles/MiscMetabar_files/sankey-1/d3-4.5.0/d3.min.js
docs/articles/MiscMetabar_files/sankey-1/sankey.js
docs/articles/MiscMetabar_files/sankeyNetwork-binding-0.4/sankeyNetwork.js
docs/articles/Reclustering.html
docs/articles/Reclustering_files/figure-html/unnamed-chunk-4-1.png
docs/articles/Reclustering_files/figure-html/unnamed-chunk-4-2.png
docs/articles/Reclustering_files/figure-html/unnamed-chunk-6-1.png
docs/articles/Reclustering_files/figure-html/unnamed-chunk-6-2.png
docs/articles/Rules.html
docs/articles/alpha-div.html
docs/articles/alpha-div_files/figure-html/unnamed-chunk-3-1.png
docs/articles/alpha-div_files/figure-html/unnamed-chunk-4-1.png
docs/articles/alpha-div_files/figure-html/unnamed-chunk-5-1.png
docs/articles/alpha-div_files/figure-html/unnamed-chunk-6-1.png
docs/articles/alpha-div_files/figure-html/unnamed-chunk-6-2.png
docs/articles/alpha-div_files/figure-html/unnamed-chunk-7-1.png
docs/articles/alpha-div_files/figure-html/unnamed-chunk-7-2.png
docs/articles/articles/Reclustering.html
docs/articles/articles/Rules.html
docs/articles/articles/alpha-div.html
docs/articles/articles/beta-div.html
docs/articles/articles/essai_article.html
docs/articles/articles/explore_data.html
docs/articles/articles/fastq_quality_check.html
docs/articles/articles/filter.html
docs/articles/articles/import_export_track.html
docs/articles/articles/quality_fastq.html
docs/articles/articles/states_of_fields_in_R.html
docs/articles/articles/tengeler.html
docs/articles/articles/tree_visualization.html
docs/articles/beta-div.html
docs/articles/beta-div_files/figure-html/unnamed-chunk-10-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-11-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-12-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-13-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-14-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-3-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-4-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-5-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-7-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-8-1.png
docs/articles/beta-div_files/figure-html/unnamed-chunk-9-1.png
docs/articles/essai_article.html
docs/articles/explore_data.html
docs/articles/explore_data_files/figure-html/unnamed-chunk-15-1.png
docs/articles/explore_data_files/figure-html/unnamed-chunk-2-1.png
docs/articles/fastq_quality_check.html
docs/articles/filter.html
docs/articles/import_export_track.html
docs/articles/index.html
docs/articles/quality_fastq.html
docs/articles/states_of_fields_in_R.html
docs/articles/tengeler.html
docs/articles/tengeler_files/figure-html/unnamed-chunk-10-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-11-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-12-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-13-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-16-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-17-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-18-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-19-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-20-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-4-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-5-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-6-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-7-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-8-1.png
docs/articles/tengeler_files/figure-html/unnamed-chunk-9-1.png
docs/articles/tree_visualization.html
docs/articles/tree_visualization_files/figure-html/unnamed-chunk-3-1.png
docs/articles/tree_visualization_files/figure-html/unnamed-chunk-3-2.png
docs/articles/tree_visualization_files/figure-html/unnamed-chunk-3-3.png
docs/articles/tree_visualization_files/figure-html/unnamed-chunk-3-4.png
docs/articles/tree_visualization_files/figure-html/unnamed-chunk-4-1.png
docs/articles/tree_visualization_files/figure-html/unnamed-chunk-4-2.png
docs/authors.html
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.3.1/bootstrap.min.css
docs/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
docs/deps/clipboard.js-2.0.11/clipboard.min.js
docs/deps/data-deps.txt
docs/deps/font-awesome-6.4.2/css/all.css
docs/deps/font-awesome-6.4.2/css/all.min.css
docs/deps/font-awesome-6.4.2/css/v4-shims.css
docs/deps/font-awesome-6.4.2/css/v4-shims.min.css
docs/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-brands-400.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-solid-900.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
docs/deps/headroom-0.11.0/headroom.min.js
docs/deps/headroom-0.11.0/jQuery.headroom.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/deps/search-1.0.0/autocomplete.jquery.min.js
docs/deps/search-1.0.0/fuse.min.js
docs/deps/search-1.0.0/mark.min.js
docs/extra.css
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/katex-auto.js
docs/lightswitch.js
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/LCBD_pq.html
docs/reference/MiscMetabar-deprecated.html
docs/reference/MiscMetabar-package.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/Rplot005.png
docs/reference/Rplot006.png
docs/reference/Rplot007.png
docs/reference/Rplot008.png
docs/reference/Rplot009.png
docs/reference/Rplot010.png
docs/reference/SRS_curve_pq-1.png
docs/reference/SRS_curve_pq-2.png
docs/reference/SRS_curve_pq.html
docs/reference/Tengeler2020_pq.html
docs/reference/accu_plot-1.png
docs/reference/accu_plot-2.png
docs/reference/accu_plot.html
docs/reference/accu_plot_balanced_modality-1.png
docs/reference/accu_plot_balanced_modality-2.png
docs/reference/accu_plot_balanced_modality.html
docs/reference/accu_samp_threshold-1.png
docs/reference/accu_samp_threshold.html
docs/reference/add_blast_info.html
docs/reference/add_dna_to_phyloseq.html
docs/reference/add_funguild_info.html
docs/reference/add_info_to_sam_data-1.png
docs/reference/add_info_to_sam_data-2.png
docs/reference/add_info_to_sam_data.html
docs/reference/add_new_taxonomy_pq.html
docs/reference/adonis_phyloseq.html
docs/reference/adonis_pq.html
docs/reference/adonis_rarperm_pq.html
docs/reference/all_object_size.html
docs/reference/ancombc_pq-1.png
docs/reference/ancombc_pq.html
docs/reference/are_modality_even_depth-1.png
docs/reference/are_modality_even_depth.html
docs/reference/as_binary_otu_table.html
docs/reference/asv2otu.html
docs/reference/bad_flush_right.html
docs/reference/bad_or_unique.html
docs/reference/biplot_physeq.html
docs/reference/biplot_pq-1.png
docs/reference/biplot_pq.html
docs/reference/blast_pq.html
docs/reference/blast_to_derep.html
docs/reference/blast_to_phyloseq.html
docs/reference/build_phytree_pq-1.png
docs/reference/build_phytree_pq-2.png
docs/reference/build_phytree_pq-3.png
docs/reference/build_phytree_pq-4.png
docs/reference/build_phytree_pq-5.png
docs/reference/build_phytree_pq-6.png
docs/reference/build_phytree_pq-7.png
docs/reference/build_phytree_pq-8.png
docs/reference/build_phytree_pq.html
docs/reference/chimera_detection_vs.html
docs/reference/chimera_removal_vs.html
docs/reference/circle_pq-1.png
docs/reference/circle_pq-2.png
docs/reference/circle_pq-3.png
docs/reference/circle_pq.html
docs/reference/clean_physeq.html
docs/reference/clean_pq.html
docs/reference/compare_pairs_pq.html
docs/reference/count_seq.html
docs/reference/cutadapt_remove_primers.html
docs/reference/data_fungi.html
docs/reference/data_fungi_mini.html
docs/reference/data_fungi_sp_known.html
docs/reference/diff_fct_diff_class.html
docs/reference/dist_bycol.html
docs/reference/dist_pos_control-1.png
docs/reference/dist_pos_control.html
docs/reference/distri_1_taxa.html
docs/reference/fac2col.html
docs/reference/figures/README-example-1.png
docs/reference/figures/README-unnamed-chunk-2-1.png
docs/reference/figures/README-unnamed-chunk-3-1.png
docs/reference/figures/README-unnamed-chunk-4-1.png
docs/reference/figures/README-unnamed-chunk-5-1.png
docs/reference/figures/README-unnamed-chunk-6-1.png
docs/reference/figures/README-unnamed-chunk-6-2.png
docs/reference/figures/README-unnamed-chunk-6-3.png
docs/reference/figures/README-unnamed-chunk-7-1.png
docs/reference/figures/README-unnamed-chunk-8-1.png
docs/reference/figures/README-unnamed-chunk-8-2.png
docs/reference/figures/lifecycle-archived.svg
docs/reference/figures/lifecycle-defunct.svg
docs/reference/figures/lifecycle-deprecated.svg
docs/reference/figures/lifecycle-experimental.svg
docs/reference/figures/lifecycle-maturing.svg
docs/reference/figures/lifecycle-questioning.svg
docs/reference/figures/lifecycle-stable.svg
docs/reference/figures/lifecycle-superseded.svg
docs/reference/figures/logo.png
docs/reference/filter_asv_blast.html
docs/reference/filter_taxa_blast.html
docs/reference/filter_trim.html
docs/reference/formattable_pq.html
docs/reference/funguild_assign.html
docs/reference/funky_color.html
docs/reference/get_file_extension.html
docs/reference/get_funguild_db.html
docs/reference/ggVenn_phyloseq.html
docs/reference/ggaluv_pq-1.png
docs/reference/ggaluv_pq-2.png
docs/reference/ggaluv_pq.html
docs/reference/ggbetween_pq-1.png
docs/reference/ggbetween_pq-2.png
docs/reference/ggbetween_pq-3.png
docs/reference/ggbetween_pq.html
docs/reference/ggscatt_pq-1.png
docs/reference/ggscatt_pq-2.png
docs/reference/ggscatt_pq.html
docs/reference/ggvenn_pq-1.png
docs/reference/ggvenn_pq-10.png
docs/reference/ggvenn_pq-2.png
docs/reference/ggvenn_pq-3.png
docs/reference/ggvenn_pq-4.png
docs/reference/ggvenn_pq-5.png
docs/reference/ggvenn_pq-6.png
docs/reference/ggvenn_pq-7.png
docs/reference/ggvenn_pq-8.png
docs/reference/ggvenn_pq-9.png
docs/reference/ggvenn_pq.html
docs/reference/glmutli_pq.html
docs/reference/graph_test_pq-1.png
docs/reference/graph_test_pq-2.png
docs/reference/graph_test_pq.html
docs/reference/heat_tree_pq-1.png
docs/reference/heat_tree_pq.html
docs/reference/hill_phyloseq.html
docs/reference/hill_pq-1.png
docs/reference/hill_pq-2.png
docs/reference/hill_pq.html
docs/reference/hill_test_rarperm_pq.html
docs/reference/hill_tuckey_phyloseq.html
docs/reference/hill_tuckey_pq-1.png
docs/reference/hill_tuckey_pq-2.png
docs/reference/hill_tuckey_pq.html
docs/reference/iNEXT_pq.html
docs/reference/index.html
docs/reference/install_pkg_needed.html
docs/reference/is_cutadapt_installed.html
docs/reference/is_falco_installed.html
docs/reference/is_krona_installed.html
docs/reference/is_mumu_installed.html
docs/reference/is_swarm_installed.html
docs/reference/is_vsearch_installed.html
docs/reference/krona.html
docs/reference/libs/crosstalk-1.2.0/css/crosstalk.min.css
docs/reference/libs/crosstalk-1.2.0/js/crosstalk.js
docs/reference/libs/crosstalk-1.2.0/js/crosstalk.js.map
docs/reference/libs/crosstalk-1.2.0/js/crosstalk.min.js
docs/reference/libs/crosstalk-1.2.0/js/crosstalk.min.js.map
docs/reference/libs/crosstalk-1.2.0/scss/crosstalk.scss
docs/reference/libs/crosstalk-1.2.1/css/crosstalk.min.css
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.js
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.js.map
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.min.js
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/reference/libs/crosstalk-1.2.1/scss/crosstalk.scss
docs/reference/libs/d3-4.5.0/LICENSE
docs/reference/libs/d3-4.5.0/d3.min.js
docs/reference/libs/datatables-binding-0.30/datatables.js
docs/reference/libs/datatables-binding-0.31/datatables.js
docs/reference/libs/datatables-binding-0.32/datatables.js
docs/reference/libs/datatables-binding-0.32/fastqc_data.txt
docs/reference/libs/datatables-binding-0.32/fastqc_report.html
docs/reference/libs/datatables-binding-0.32/summary.txt
docs/reference/libs/datatables-binding-0.33/datatables.js
docs/reference/libs/datatables-css-0.0.0/datatables-crosstalk.css
docs/reference/libs/dt-core-1.13.4/css/jquery.dataTables.extra.css
docs/reference/libs/dt-core-1.13.4/css/jquery.dataTables.min.css
docs/reference/libs/dt-core-1.13.4/js/jquery.dataTables.min.js
docs/reference/libs/dt-core-1.13.6/css/jquery.dataTables.extra.css
docs/reference/libs/dt-core-1.13.6/css/jquery.dataTables.min.css
docs/reference/libs/dt-core-1.13.6/js/jquery.dataTables.min.js
docs/reference/libs/htmlwidgets-1.6.2/htmlwidgets.js
docs/reference/libs/htmlwidgets-1.6.4/htmlwidgets.js
docs/reference/libs/sankey-1/d3-4.5.0/LICENSE
docs/reference/libs/sankey-1/d3-4.5.0/d3.min.js
docs/reference/libs/sankey-1/sankey.js
docs/reference/libs/sankeyNetwork-binding-0.4/sankeyNetwork.js
docs/reference/list_fastq_files.html
docs/reference/lulu.html
docs/reference/lulu_phyloseq.html
docs/reference/lulu_pq.html
docs/reference/merge_groups.html
docs/reference/merge_krona.html
docs/reference/merge_samples2,otu_table-method.html
docs/reference/merge_samples2,phyloseq-method.html
docs/reference/merge_samples2,sample_data-method.html
docs/reference/merge_samples2.html
docs/reference/merge_taxa_vec,XStringSet-method.html
docs/reference/merge_taxa_vec,otu_table-method.html
docs/reference/merge_taxa_vec,phylo-method.html
docs/reference/merge_taxa_vec,phyloseq-method.html
docs/reference/merge_taxa_vec,taxonomyTable-method.html
docs/reference/merge_taxa_vec.html
docs/reference/merge_taxa_vec_pseudo.html
docs/reference/multi_biplot_pq-1.png
docs/reference/multi_biplot_pq-2.png
docs/reference/multi_biplot_pq.html
docs/reference/multipatt_pq-1.png
docs/reference/multipatt_pq-2.png
docs/reference/multipatt_pq.html
docs/reference/multiplot.html
docs/reference/multitax_bar_pq-1.png
docs/reference/multitax_bar_pq-2.png
docs/reference/multitax_bar_pq-3.png
docs/reference/multitax_bar_pq.html
docs/reference/mumu_pq.html
docs/reference/normalize_prop_pq-1.png
docs/reference/normalize_prop_pq.html
docs/reference/otu_circle.html
docs/reference/perc.html
docs/reference/phyloseq_to_edgeR.html
docs/reference/physeq_graph_test.html
docs/reference/physeq_heat_tree.html
docs/reference/physeq_or_string_to_dna.html
docs/reference/plot_LCBD_pq-1.png
docs/reference/plot_LCBD_pq-2.png
docs/reference/plot_LCBD_pq-3.png
docs/reference/plot_LCBD_pq-4.png
docs/reference/plot_LCBD_pq.html
docs/reference/plot_SCBD_pq-1.png
docs/reference/plot_SCBD_pq-2.png
docs/reference/plot_SCBD_pq.html
docs/reference/plot_ancombc_pq-1.png
docs/reference/plot_ancombc_pq-2.png
docs/reference/plot_ancombc_pq-3.png
docs/reference/plot_ancombc_pq.html
docs/reference/plot_deseq2_phyloseq.html
docs/reference/plot_deseq2_pq-1.png
docs/reference/plot_deseq2_pq-2.png
docs/reference/plot_deseq2_pq.html
docs/reference/plot_edgeR_phyloseq.html
docs/reference/plot_edgeR_pq-1.png
docs/reference/plot_edgeR_pq-2.png
docs/reference/plot_edgeR_pq.html
docs/reference/plot_guild_pq-1.png
docs/reference/plot_guild_pq.html
docs/reference/plot_mt-1.png
docs/reference/plot_mt-2.png
docs/reference/plot_mt.html
docs/reference/plot_tax_pq-1.png
docs/reference/plot_tax_pq-2.png
docs/reference/plot_tax_pq-3.png
docs/reference/plot_tax_pq.html
docs/reference/plot_tsne_pq-1.png
docs/reference/plot_tsne_pq-2.png
docs/reference/plot_tsne_pq-3.png
docs/reference/plot_tsne_pq.html
docs/reference/plot_var_part_pq-1.png
docs/reference/plot_var_part_pq-2.png
docs/reference/plot_var_part_pq-3.png
docs/reference/plot_var_part_pq.html
docs/reference/postcluster_pq.html
docs/reference/psmelt_samples_pq-1.png
docs/reference/psmelt_samples_pq-2.png
docs/reference/psmelt_samples_pq-3.png
docs/reference/psmelt_samples_pq-4.png
docs/reference/psmelt_samples_pq.html
docs/reference/rarefy_sample_count_by_modality-1.png
docs/reference/rarefy_sample_count_by_modality.html
docs/reference/read_phyloseq.html
docs/reference/read_pq.html
docs/reference/rename_samples.html
docs/reference/rename_samples_otu_table.html
docs/reference/reorder_taxa_pq.html
docs/reference/ridges_pq-1.png
docs/reference/ridges_pq-2.png
docs/reference/ridges_pq-3.png
docs/reference/ridges_pq-4.png
docs/reference/ridges_pq-5.png
docs/reference/ridges_pq-6.png
docs/reference/ridges_pq.html
docs/reference/rotl_pq-1.png
docs/reference/rotl_pq-2.png
docs/reference/rotl_pq.html
docs/reference/sample_data_stable.html
docs/reference/sample_data_with_new_names.html
docs/reference/sankey_phyloseq.html
docs/reference/sankey_pq.html
docs/reference/save_pq.html
docs/reference/search_exact_seq_pq.html
docs/reference/select_one_sample.html
docs/reference/select_taxa,XStringSet,character-method.html
docs/reference/select_taxa,otu_table,character-method.html
docs/reference/select_taxa,phylo,character-method.html
docs/reference/select_taxa,phyloseq,character-method.html
docs/reference/select_taxa,sample_data,character-method.html
docs/reference/select_taxa,taxonomyTable,character-method.html
docs/reference/select_taxa-methods.html
docs/reference/signif_ancombc.html
docs/reference/simplify_taxo.html
docs/reference/subsample_fastq.html
docs/reference/subset_samples_pq.html
docs/reference/subset_taxa_pq.html
docs/reference/subset_taxa_tax_control.html
docs/reference/summary_plot_phyloseq.html
docs/reference/summary_plot_pq-1.png
docs/reference/summary_plot_pq-2.png
docs/reference/summary_plot_pq.html
docs/reference/swarm_clustering-1.png
docs/reference/swarm_clustering-2.png
docs/reference/swarm_clustering.html
docs/reference/tax_bar_pq-1.png
docs/reference/tax_bar_pq-2.png
docs/reference/tax_bar_pq-3.png
docs/reference/tax_bar_pq-4.png
docs/reference/tax_bar_pq.html
docs/reference/tax_datatable.html
docs/reference/taxa_as_columns.html
docs/reference/taxa_as_rows.html
docs/reference/taxa_only_in_one_level.html
docs/reference/tbl_sum_samdata.html
docs/reference/track_wkflow.html
docs/reference/track_wkflow_samples.html
docs/reference/transp.html
docs/reference/treemap_pq-1.png
docs/reference/treemap_pq-2.png
docs/reference/treemap_pq-3.png
docs/reference/treemap_pq.html
docs/reference/tsne_pq.html
docs/reference/unique_or_na.html
docs/reference/upset_pq-1.png
docs/reference/upset_pq-10.png
docs/reference/upset_pq-2.png
docs/reference/upset_pq-3.png
docs/reference/upset_pq-4.png
docs/reference/upset_pq-5.png
docs/reference/upset_pq-6.png
docs/reference/upset_pq-7.png
docs/reference/upset_pq-8.png
docs/reference/upset_pq-9.png
docs/reference/upset_pq.html
docs/reference/upset_test_pq.html
docs/reference/var_par_pq.html
docs/reference/var_par_rarperm_pq.html
docs/reference/venn_phyloseq.html
docs/reference/venn_pq-1.png
docs/reference/venn_pq-2.png
docs/reference/venn_pq-3.png
docs/reference/venn_pq-4.png
docs/reference/venn_pq-5.png
docs/reference/venn_pq.html
docs/reference/verify_pq.html
docs/reference/vs_search_global.html
docs/reference/vsearch_clustering-1.png
docs/reference/vsearch_clustering-2.png
docs/reference/vsearch_clustering.html
docs/reference/write_phyloseq.html
docs/reference/write_pq.html
docs/search.json
docs/sitemap.xml
inst/extdata/100_sp_UNITE_sh_general_release_dynamic.fasta
inst/extdata/dbase.ndb
inst/extdata/dbase.nhr
inst/extdata/dbase.nin
inst/extdata/dbase.not
inst/extdata/dbase.nsq
inst/extdata/dbase.ntf
inst/extdata/dbase.nto
inst/extdata/ex.fasta
inst/extdata/ex.fastq
inst/extdata/ex_R1_001.fasta
inst/extdata/ex_R1_001.fastq.gz
inst/extdata/ex_R1_002.fasta
inst/extdata/ex_R2_001.fastq.gz
inst/extdata/ex_little.fasta
inst/extdata/sam_data.csv
man/LCBD_pq.Rd man/MiscMetabar-deprecated.Rd man/MiscMetabar-package.Rd man/SRS_curve_pq.Rd man/Tengeler2020_pq.Rd man/accu_plot.Rd man/accu_plot_balanced_modality.Rd man/accu_samp_threshold.Rd man/add_blast_info.Rd man/add_dna_to_phyloseq.Rd man/add_funguild_info.Rd man/add_info_to_sam_data.Rd man/add_new_taxonomy_pq.Rd man/adonis_pq.Rd man/adonis_rarperm_pq.Rd man/all_object_size.Rd man/ancombc_pq.Rd man/are_modality_even_depth.Rd man/as_binary_otu_table.Rd man/biplot_pq.Rd man/blast_pq.Rd man/blast_to_derep.Rd man/blast_to_phyloseq.Rd man/build_phytree_pq.Rd man/chimera_detection_vs.Rd man/chimera_removal_vs.Rd man/circle_pq.Rd man/clean_pq.Rd man/compare_pairs_pq.Rd man/count_seq.Rd man/cutadapt_remove_primers.Rd man/data_fungi.Rd man/data_fungi_mini.Rd man/data_fungi_sp_known.Rd man/diff_fct_diff_class.Rd man/dist_bycol.Rd man/dist_pos_control.Rd man/distri_1_taxa.Rd man/fac2col.Rd
man/figures/README-example-1.png
man/figures/README-unnamed-chunk-4-1.png
man/figures/README-unnamed-chunk-5-1.png
man/figures/README-unnamed-chunk-6-1.png
man/figures/README-unnamed-chunk-7-1.png
man/figures/README-unnamed-chunk-8-1.png
man/filter_asv_blast.Rd man/filter_trim.Rd man/formattable_pq.Rd man/funguild_assign.Rd man/funky_color.Rd man/get_file_extension.Rd man/get_funguild_db.Rd man/ggaluv_pq.Rd man/ggbetween_pq.Rd man/ggscatt_pq.Rd man/ggvenn_pq.Rd man/glmutli_pq.Rd man/graph_test_pq.Rd man/hill_pq.Rd man/hill_test_rarperm_pq.Rd man/hill_tuckey_pq.Rd man/iNEXT_pq.Rd man/is_cutadapt_installed.Rd man/is_falco_installed.Rd man/is_krona_installed.Rd man/is_mumu_installed.Rd man/is_swarm_installed.Rd man/is_vsearch_installed.Rd man/krona.Rd man/list_fastq_files.Rd man/lulu.Rd man/lulu_pq.Rd man/merge_krona.Rd man/merge_samples2.Rd man/merge_taxa_vec.Rd man/multi_biplot_pq.Rd man/multipatt_pq.Rd man/multiplot.Rd man/multitax_bar_pq.Rd man/mumu_pq.Rd man/normalize_prop_pq.Rd man/perc.Rd man/phyloseq_to_edgeR.Rd man/physeq_or_string_to_dna.Rd man/plot_LCBD_pq.Rd man/plot_SCBD_pq.Rd man/plot_ancombc_pq.Rd man/plot_deseq2_pq.Rd man/plot_edgeR_pq.Rd man/plot_guild_pq.Rd man/plot_mt.Rd man/plot_tax_pq.Rd man/plot_tsne_pq.Rd man/plot_var_part_pq.Rd man/postcluster_pq.Rd man/psmelt_samples_pq.Rd man/rarefy_sample_count_by_modality.Rd man/read_pq.Rd man/rename_samples.Rd man/rename_samples_otu_table.Rd man/reorder_taxa_pq.Rd man/ridges_pq.Rd man/rotl_pq.Rd man/sample_data_with_new_names.Rd man/sankey_pq.Rd man/save_pq.Rd man/search_exact_seq_pq.Rd man/select_one_sample.Rd man/select_taxa-methods.Rd man/signif_ancombc.Rd man/simplify_taxo.Rd man/subsample_fastq.Rd man/subset_samples_pq.Rd man/subset_taxa_pq.Rd man/subset_taxa_tax_control.Rd man/summary_plot_pq.Rd man/swarm_clustering.Rd man/tax_bar_pq.Rd man/tax_datatable.Rd man/taxa_as_columns.Rd man/taxa_as_rows.Rd man/taxa_only_in_one_level.Rd man/tbl_sum_samdata.Rd man/track_wkflow.Rd man/track_wkflow_samples.Rd man/transp.Rd man/treemap_pq.Rd man/tsne_pq.Rd man/unique_or_na.Rd man/upset_pq.Rd man/upset_test_pq.Rd man/var_par_pq.Rd man/var_par_rarperm_pq.Rd man/venn_pq.Rd man/verify_pq.Rd man/vs_search_global.Rd man/vsearch_clustering.Rd man/write_pq.Rd
paper/bibliography.bib
paper/figures_svg/description_MiscMetabar.svg
paper/figures_svg/table1.svg
paper/figures_svg/table1_publication.svg
paper/figures_svg/table_1old.svg
paper/figures_svg/tengeler_MiscMetabar.svg
paper/figures_svg/tengeler_MiscMetabar_editable.svg
paper/paper.bib
paper/paper.md paper/paper_old.md
paper/table1_publication.svg
paper/tengeler_MiscMetabar.svg
pkgdown/extra.css
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/testthat.R tests/testthat/Rplots.pdf
tests/testthat/inst/extdata/1000_sp_UNITE_sh_general_release_dynamic.fasta
tests/testthat/inst/extdata/dbase.ndb
tests/testthat/inst/extdata/dbase.nhr
tests/testthat/inst/extdata/dbase.nin
tests/testthat/inst/extdata/dbase.not
tests/testthat/inst/extdata/dbase.nsq
tests/testthat/inst/extdata/dbase.ntf
tests/testthat/inst/extdata/dbase.nto
tests/testthat/inst/extdata/ex.fasta
tests/testthat/inst/extdata/ex.fastq
tests/testthat/inst/extdata/ex_R1_001.fastq.gz
tests/testthat/inst/extdata/ex_R2_001.fastq.gz
tests/testthat/inst/extdata/ex_little.fasta
tests/testthat/log.txt
tests/testthat/test_adonis.R tests/testthat/test_blast.R tests/testthat/test_clean_pq.R tests/testthat/test_controls.R tests/testthat/test_cutadapt.R tests/testthat/test_deprecated.R tests/testthat/test_deseq2_edgeR.R tests/testthat/test_figures_alpha_div.R tests/testthat/test_figures_beta_div.R tests/testthat/test_figures_biplot.R tests/testthat/test_figures_misc.R tests/testthat/test_figures_summary_plot.R tests/testthat/test_figures_taxo.R tests/testthat/test_krona.R tests/testthat/test_misc.R tests/testthat/test_phyloseq_class.R tests/testthat/test_rw.R tests/testthat/test_subset.R tests/testthat/test_swarm.R tests/testthat/test_table_functions.R tests/testthat/test_targets.R tests/testthat/test_tuckey.R tests/testthat/test_vsearch.R
vignettes/.gitignore
vignettes/MiscMetabar.Rmd vignettes/articles/Reclustering.Rmd vignettes/articles/Rules.Rmd vignettes/articles/alpha-div.Rmd vignettes/articles/beta-div.Rmd
vignettes/articles/bibliography.bib
vignettes/articles/explore_data.Rmd vignettes/articles/fastq_quality_check.Rmd vignettes/articles/filter.Rmd vignettes/articles/import_export_track.Rmd vignettes/articles/states_of_fields_in_R.Rmd vignettes/articles/tengeler.Rmd vignettes/articles/tree_visualization.Rmd
vignettes/bibliography.bib
adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.