Files in vmikk/metagMisc
Miscellaneous functions for metagenomic analysis
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
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
figures/Logo_metagMisc.png
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
vignettes/Diversity_profile.png
vignettes/Filter_top_taxa.png
vignettes/Pairwise_dissimilarity_boxplot.png
vignettes/Prevalence_plots.png
vignettes/Taxonomic_resolution.png
