Files in MiscMetabar

Miscellaneous Functions for Metabarcoding Analysis

NEWS.md README.md R/speedyseq_functions.R R/targets_misc.R R/dada_phyloseq.R R/table_functions.R R/krona.R R/plot_functions.R R/data.R R/controls.R R/deprecated.R R/Deseq2_edgeR.R R/vsearch.R R/blast.R R/beta_div_test.R R/MiscMetabar-package.R R/alpha_div_test.R R/lulu.R R/funguild.R R/miscellanous.R inst/doc/MiscMetabar.R inst/doc/MiscMetabar.Rmd tests/testthat.R tests/testthat/test_krona.R tests/testthat/test_adonis.R tests/testthat/test_deseq2_edgeR.R tests/testthat/test_figures_summary_plot.R tests/testthat/test_cutadapt.R tests/testthat/test_subset.R tests/testthat/test_figures_taxo.R tests/testthat/test_clean_pq.R tests/testthat/test_misc.R tests/testthat/test_controls.R tests/testthat/test_swarm.R tests/testthat/test_deprecated.R tests/testthat/test_rw.R tests/testthat/Rplots.pdf tests/testthat/test_figures_beta_div.R tests/testthat/test_figures_misc.R tests/testthat/test_table_functions.R tests/testthat/test_tuckey.R tests/testthat/test_blast.R tests/testthat/test_phyloseq_class.R tests/testthat/test_figures_biplot.R tests/testthat/test_figures_alpha_div.R tests/testthat/test_vsearch.R tests/testthat/test_targets.R vignettes/MiscMetabar.Rmd man/blast_pq.Rd man/vs_search_global.Rd man/save_pq.Rd man/MiscMetabar-package.Rd man/venn_pq.Rd man/are_modality_even_depth.Rd man/select_taxa-methods.Rd man/multiplot.Rd man/ancombc_pq.Rd man/add_new_taxonomy_pq.Rd man/data_fungi.Rd man/blast_to_phyloseq.Rd man/psmelt_samples_pq.Rd man/plot_edgeR_pq.Rd man/accu_plot_balanced_modality.Rd man/mumu_pq.Rd man/plot_guild_pq.Rd man/add_funguild_info.Rd man/plot_mt.Rd man/compare_pairs_pq.Rd man/distri_1_taxa.Rd man/plot_SCBD_pq.Rd man/get_file_extension.Rd man/fac2col.Rd man/chimera_removal_vs.Rd man/read_pq.Rd man/tbl_sum_samdata.Rd man/graph_test_pq.Rd man/ggscatt_pq.Rd man/tsne_pq.Rd man/multipatt_pq.Rd man/accu_samp_threshold.Rd man/swarm_clustering.Rd man/signif_ancombc.Rd man/build_phytree_pq.Rd man/merge_taxa_vec.Rd man/taxa_as_rows.Rd man/sample_data_with_new_names.Rd man/adonis_rarperm_pq.Rd man/verify_pq.Rd man/var_par_rarperm_pq.Rd man/rename_samples.Rd man/list_fastq_files.Rd man/iNEXT_pq.Rd man/multitax_bar_pq.Rd man/perc.Rd man/taxa_as_columns.Rd man/taxa_only_in_one_level.Rd man/clean_pq.Rd man/LCBD_pq.Rd man/heat_tree_pq.Rd man/track_wkflow.Rd man/reorder_taxa_pq.Rd man/accu_plot.Rd man/treemap_pq.Rd man/krona.Rd man/merge_samples2.Rd man/add_dna_to_phyloseq.Rd man/hill_test_rarperm_pq.Rd man/add_info_to_sam_data.Rd man/dist_pos_control.Rd man/dist_bycol.Rd man/data_fungi_mini.Rd man/is_cutadapt_installed.Rd man/phyloseq_to_edgeR.Rd man/var_par_pq.Rd man/subset_samples_pq.Rd man/hill_pq.Rd man/ggaluv_pq.Rd man/physeq_or_string_to_dna.Rd man/get_funguild_db.Rd man/all_object_size.Rd man/tax_bar_pq.Rd man/plot_var_part_pq.Rd man/funky_color.Rd man/cutadapt_remove_primers.Rd man/is_falco_installed.Rd man/merge_krona.Rd man/ridges_pq.Rd man/MiscMetabar-deprecated.Rd man/plot_tsne_pq.Rd man/upset_pq.Rd man/multi_biplot_pq.Rd man/is_krona_installed.Rd man/search_exact_seq_pq.Rd man/is_vsearch_installed.Rd man/postcluster_pq.Rd man/simplify_taxo.Rd man/rotl_pq.Rd man/upset_test_pq.Rd man/unique_or_na.Rd man/rarefy_sample_count_by_modality.Rd man/normalize_prop_pq.Rd man/summary_plot_pq.Rd man/is_mumu_installed.Rd man/tax_datatable.Rd man/circle_pq.Rd man/subsample_fastq.Rd man/sankey_pq.Rd man/lulu_pq.Rd man/select_one_sample.Rd man/subset_taxa_pq.Rd man/plot_LCBD_pq.Rd man/diff_fct_diff_class.Rd man/biplot_pq.Rd man/data_fungi_sp_known.Rd man/rename_samples_otu_table.Rd man/hill_tuckey_pq.Rd man/subset_taxa_tax_control.Rd man/chimera_detection_vs.Rd man/adonis_pq.Rd man/is_swarm_installed.Rd man/glmutli_pq.Rd man/lulu.Rd man/transp.Rd man/filter_asv_blast.Rd man/funguild_assign.Rd man/plot_deseq2_pq.Rd man/ggvenn_pq.Rd man/add_blast_info.Rd man/SRS_curve_pq.Rd man/blast_to_derep.Rd man/plot_tax_pq.Rd man/plot_ancombc_pq.Rd man/as_binary_otu_table.Rd man/Tengeler2020_pq.Rd man/write_pq.Rd man/count_seq.Rd man/formattable_pq.Rd man/filter_trim.Rd man/ggbetween_pq.Rd man/vsearch_clustering.Rd man/track_wkflow_samples.Rd