API for vmikk/metagMisc
Miscellaneous functions for metagenomic analysis
| Global functions | |
|---|---|
| .eigen_stats | Source code |
| OTU_average | Source code |
| SES | Man page Source code |
| abbreviate_taxa_names | Man page Source code |
| add_metadata | Man page Source code |
| adonis_pairwise | Man page Source code |
| blast_to_wide | Man page Source code |
| bubble_plot | Man page Source code |
| centroid_coords | Source code |
| check_tax_uniqueness | Man page Source code |
| chunk | Source code |
| chunk_table | Source code |
| count_primers | Source code |
| coverage_to_samplesize | Source code |
| dada_learn_errors_subset | Man page Source code |
| dada_to_fasta | Man page Source code |
| dfRowName | Man page Source code |
| dissimilarity_to_distance | Man page Source code |
| dissimilarity_to_distance_importance_plot | Man page Source code |
| dist2list | Man page |
| eig_perc | Man page Source code |
| expand_CIGAR | Source code |
| extract_in_parentheses | Man page Source code |
| get_max_taxonomic_rank | Man page Source code |
| get_max_taxonomic_rank_DT | Man page Source code |
| jaccard_bray | Source code |
| leading_zero | Man page Source code |
| make_utax_taxonomy | Man page Source code |
| make_utax_taxonomy_batch | Man page Source code |
| metagenome_contributions | Man page Source code |
| multSE | Man page Source code |
| mult_dissim | Man page Source code |
| mult_dist_average | Man page Source code |
| package_availability | Source code |
| parse_amplicon_table | Man page Source code |
| parse_fastq_eestats2 | Man page Source code |
| parse_funguild | Man page Source code |
| parse_silva_tax | Man page Source code |
| parse_silva_tax_batch | Man page Source code |
| parse_swarms | Man page Source code |
| parse_taxonomy_amptk | Man page Source code |
| parse_taxonomy_amptk_batch | Man page Source code |
| parse_uc | Man page Source code |
| pd_weighted | Source code |
| phred_inverse | Man page Source code |
| phred_score | Man page Source code |
| phyloseq_add_max_tax_rank | Man page Source code |
| phyloseq_adonis | Man page Source code |
| phyloseq_average | Man page Source code |
| phyloseq_bootstrap | Source code |
| phyloseq_combine_samples | Source code |
| phyloseq_coverage | Man page Source code |
| phyloseq_coverage_raref | Man page Source code |
| phyloseq_effort_div | Source code |
| phyloseq_effort_div_rangeplot | Man page Source code |
| phyloseq_extract_non_shared_otus | Man page Source code |
| phyloseq_extract_shared_otus | Man page Source code |
| phyloseq_filter_prevalence | Man page Source code |
| phyloseq_filter_sample_wise_abund_trim | Man page Source code |
| phyloseq_filter_taxa_rel_abund | Man page Source code |
| phyloseq_filter_taxa_tot_fraction | Man page Source code |
| phyloseq_filter_test | Source code |
| phyloseq_filter_top_taxa | Man page Source code |
| phyloseq_filter_top_taxa_range | Man page Source code |
| phyloseq_group_dissimilarity | Man page Source code |
| phyloseq_inext | Man page Source code |
| phyloseq_merge_samples | Man page Source code |
| phyloseq_mult_raref | Man page Source code |
| phyloseq_mult_raref_avg | Man page Source code |
| phyloseq_mult_raref_dist | Source code |
| phyloseq_mult_raref_div | Man page Source code |
| phyloseq_ntaxa_by_tax | Man page Source code |
| phyloseq_num_shared_otus | Man page Source code |
| phyloseq_otu_appearance | Man page Source code |
| phyloseq_otu_occurrence | Man page Source code |
| phyloseq_phylo_div | Man page Source code |
| phyloseq_phylo_ses | Man page Source code |
| phyloseq_prevalence_plot | Man page Source code |
| phyloseq_randomize | Man page Source code |
| phyloseq_rename_with_tax | Man page Source code |
| phyloseq_replace_zero | Man page Source code |
| phyloseq_richness_filter | Man page Source code |
| phyloseq_rm_na_tax | Man page Source code |
| phyloseq_sep_pairwise | Man page Source code |
| phyloseq_sep_samp | Man page Source code |
| phyloseq_sep_tax | Man page Source code |
| phyloseq_sep_variable | Man page Source code |
| phyloseq_standardize_otu_abundance | Man page Source code |
| phyloseq_summary | Man page Source code |
| phyloseq_taxonomic_resolution | Man page Source code |
| phyloseq_taxonomy_imputation | Source code |
| phyloseq_to_MetaCommunity | Man page Source code |
| phyloseq_to_df | Man page Source code |
| phyloseq_transform_aldex_clr | Man page Source code |
| phyloseq_transform_css | Man page Source code |
| phyloseq_transform_rlog_blind | Man page Source code |
| phyloseq_transform_vst_blind | Man page Source code |
| physeq_transform_anderson_log | Man page Source code |
| predict_metagenomes | Man page Source code |
| prepare_breakaway | Man page Source code |
| prepare_inext | Man page Source code |
| prevalence | Man page Source code |
| raref_rtk | Man page Source code |
| read_m8 | Man page Source code |
| rtk_mod | Source code |
| shepard_plot | Man page Source code |
| some | Man page Source code |
| taxonomy_to_qiime | Man page Source code |
| uc_to_sumaclust | Man page Source code |
| vegdist_zero | Source code |
| vpd | Source code |
| weighted.var | Source code |
| zero_pad | Source code |
