API for vmikk/metagMisc
Miscellaneous functions for metagenomic analysis

Global functions
OTU_average Source code
abbreviate_taxa_names Man page Source code
add_metadata Man page Source code
adonis_pairwise Man page Source code
bubble_plot Man page Source code
check_tax_uniqueness Man page 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 Source code
eig_perc Man page Source code
eigen_stats Source code
extract_in_parentheses Man page Source code
filter_cazy Man page Source code
get_max_taxonomic_rank Man page Source code
jaccard_bray Source code
leading_zero 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_average Man page 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_mult_raref Man page Source code
phyloseq_mult_raref_avg Man page Source code
phyloseq_mult_raref_div Man page Source code
phyloseq_ntaxa_by_tax 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 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 Source code
phyloseq_to_MetaCommunity Man page Source code
phyloseq_to_df 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 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
vpd Source code
weighted.var Source code
vmikk/metagMisc documentation built on Oct. 10, 2018, 9:21 p.m.