Files in vmikk/metagMisc

Miscellaneous functions for metagenomic analysis

NEWS.md R/SES.R R/abbreviate_taxa_names.R R/add_metadata.R R/adonis_pairwise.R R/blast_to_wide.R R/bubble_plot.R R/centroid_coords.R R/check_tax_uniqueness.R R/chunk.R R/count_primers.R R/dada_learn_errors_subset.R R/dada_to_fasta.R R/dfRowName.R R/dissimilarity_to_distance.R R/dist2list.R R/eig_perc.R R/expand_CIGAR.R R/extract_in_parentheses.R R/get_max_taxonomic_rank.R R/get_max_taxonomic_rank_DT.R R/jaccard_bray.R R/leading_zero.R R/make_utax_taxonomy.R R/metagenome_contributions.R R/multSE.R R/package_availability.R R/parse_amplicon_table.R R/parse_amptk_taxonomy_table.R R/parse_fastq_eestats2.R R/parse_funguild.R R/parse_silva.R R/parse_swarms.R R/parse_uc.R R/phred_scores.R R/phyloseq_add_max_tax_rank.R R/phyloseq_adonis.R R/phyloseq_average.R R/phyloseq_bootstrap.R R/phyloseq_combine_samples.R R/phyloseq_coverage.R R/phyloseq_effort.R R/phyloseq_extract_otus.R R/phyloseq_filter.R R/phyloseq_filter_test.R R/phyloseq_group_dissimilarity.R R/phyloseq_inext.R R/phyloseq_merge_samples.R R/phyloseq_mult_dist.R R/phyloseq_mult_raref.R R/phyloseq_mult_raref_avg.R R/phyloseq_mult_raref_div.R R/phyloseq_ntaxa_by_tax.R R/phyloseq_num_shared_otus.R R/phyloseq_otu_occurrence.R R/phyloseq_phylo_div.R R/phyloseq_phylo_ses.R R/phyloseq_prevalence_plot.R R/phyloseq_randomize.R R/phyloseq_rename_with_tax.R R/phyloseq_sep_pairwise.R R/phyloseq_sep_samp.R R/phyloseq_sep_tax.R R/phyloseq_sep_variable.R R/phyloseq_standardize_otu_abundance.R R/phyloseq_summary.R R/phyloseq_taxonomic_resolution.R R/phyloseq_taxonomy_imputation.R R/phyloseq_to_MetaCommunity.R R/phyloseq_to_df.R R/phyloseq_transform.R R/physeq_rm_na_tax.R R/predict_metagenomes.R R/prepare_breakaway.R R/prepare_inext.R R/prevalence.R R/raref_rtk.R R/read_m8.R R/shepard_plot.R R/some.R R/taxonomy_to_qiime.R R/uc_to_sumaclust.R R/vegdist_zero.R R/zero_pad.R README.md inst/tinytest/test_SES.R inst/tinytest/test_dfRowName.R inst/tinytest/test_dist2list.R inst/tinytest/test_leading_zero.R inst/tinytest/test_zero_pad.R man/SES.Rd man/abbreviate_taxa_names.Rd man/add_metadata.Rd man/adonis_pairwise.Rd man/blast_to_wide.Rd man/bubble_plot.Rd man/check_tax_uniqueness.Rd man/dada_learn_errors_subset.Rd man/dada_to_fasta.Rd man/dfRowName.Rd man/dissimilarity_to_distance.Rd man/dissimilarity_to_distance_importance_plot.Rd man/dist2list.Rd man/eig_perc.Rd man/extract_in_parentheses.Rd man/get_max_taxonomic_rank.Rd man/get_max_taxonomic_rank_DT.Rd man/leading_zero.Rd man/make_utax_taxonomy.Rd man/make_utax_taxonomy_batch.Rd man/metagenome_contributions.Rd man/multSE.Rd man/mult_dissim.Rd man/mult_dist_average.Rd man/parse_amplicon_table.Rd man/parse_fastq_eestats2.Rd man/parse_funguild.Rd man/parse_silva_tax.Rd man/parse_silva_tax_batch.Rd man/parse_swarms.Rd man/parse_taxonomy_amptk.Rd man/parse_taxonomy_amptk_batch.Rd man/parse_uc.Rd man/phred_inverse.Rd man/phred_score.Rd man/phyloseq_add_max_tax_rank.Rd man/phyloseq_adonis.Rd man/phyloseq_average.Rd man/phyloseq_coverage.Rd man/phyloseq_coverage_raref.Rd man/phyloseq_effort_div_rangeplot.Rd man/phyloseq_extract_non_shared_otus.Rd man/phyloseq_extract_shared_otus.Rd man/phyloseq_filter_prevalence.Rd man/phyloseq_filter_sample_wise_abund_trim.Rd man/phyloseq_filter_taxa_rel_abund.Rd man/phyloseq_filter_taxa_tot_fraction.Rd man/phyloseq_filter_top_taxa.Rd man/phyloseq_filter_top_taxa_range.Rd man/phyloseq_group_dissimilarity.Rd man/phyloseq_inext.Rd man/phyloseq_merge_samples.Rd man/phyloseq_mult_raref.Rd man/phyloseq_mult_raref_avg.Rd man/phyloseq_mult_raref_div.Rd man/phyloseq_ntaxa_by_tax.Rd man/phyloseq_num_shared_otus.Rd man/phyloseq_otu_appearance.Rd man/phyloseq_otu_occurrence.Rd man/phyloseq_phylo_div.Rd man/phyloseq_phylo_ses.Rd man/phyloseq_prevalence_plot.Rd man/phyloseq_randomize.Rd man/phyloseq_rename_with_tax.Rd man/phyloseq_replace_zero.Rd man/phyloseq_richness_filter.Rd man/phyloseq_rm_na_tax.Rd man/phyloseq_sep_pairwise.Rd man/phyloseq_sep_samp.Rd man/phyloseq_sep_tax.Rd man/phyloseq_sep_variable.Rd man/phyloseq_standardize_otu_abundance.Rd man/phyloseq_summary.Rd man/phyloseq_taxonomic_resolution.Rd man/phyloseq_to_MetaCommunity.Rd man/phyloseq_to_df.Rd man/phyloseq_transform_aldex_clr.Rd man/phyloseq_transform_css.Rd man/phyloseq_transform_rlog_blind.Rd man/phyloseq_transform_vst_blind.Rd man/physeq_transform_anderson_log.Rd man/predict_metagenomes.Rd man/prepare_breakaway.Rd man/prepare_inext.Rd man/prevalence.Rd man/raref_rtk.Rd man/read_m8.Rd man/shepard_plot.Rd man/some.Rd man/taxonomy_to_qiime.Rd man/uc_to_sumaclust.Rd tests/tinytest.R