Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data


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Documentation for package ‘metacoder’ version 0.3.4

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ambiguous_synonyms Get patterns for ambiguous taxa
as_phyloseq Convert taxmap to phyloseq
calc_group_mean Calculate means of groups of columns
calc_group_median Calculate medians of groups of columns
calc_group_rsd Relative standard deviations of groups of columns
calc_group_stat Apply a function to groups of columns
calc_n_samples Count the number of samples
calc_obs_props Calculate proportions from observation counts
calc_prop_samples Calculate the proportion of samples
compare_groups Compare groups of samples
complement Find complement of sequences
counts_to_presence Apply a function to groups of columns
diverging_palette The default diverging color palette
filter_ambiguous_taxa Filter ambiguous taxon names
heat_tree Plot a taxonomic tree
heat_tree.default Plot a taxonomic tree
heat_tree.Taxmap Plot a taxonomic tree
heat_tree_matrix Plot a matrix of heat trees
hmp_otus A HMP subset
hmp_samples Sample information for HMP subset
is_ambiguous Find ambiguous taxon names
layout_functions Layout functions
make_dada2_asv_table Make a imitation of the dada2 ASV abundance matrix
make_dada2_tax_table Make a imitation of the dada2 taxonomy matrix
metacoder Metacoder
ncbi_taxon_sample Download representative sequences for a taxon
parse_dada2 Convert the output of dada2 to a taxmap object
parse_greengenes Parse Greengenes release
parse_mothur_taxonomy Parse mothur Classify.seqs *.taxonomy output
parse_mothur_tax_summary Parse mothur *.tax.summary Classify.seqs output
parse_newick Parse a Newick file
parse_phylo Parse a phylo object
parse_phyloseq Convert a phyloseq to taxmap
parse_qiime_biom Parse a BIOM output from QIIME
parse_rdp Parse RDP FASTA release
parse_silva_fasta Parse SILVA FASTA release
parse_ubiome Converts the uBiome file format to taxmap
parse_unite_general Parse UNITE general release FASTA
primersearch Use EMBOSS primersearch for in silico PCR
primersearch_raw Use EMBOSS primersearch for in silico PCR
qualitative_palette The default qualitative color palette
quantative_palette The default quantative color palette
rarefy_obs Calculate rarefied observation counts
read_fasta Read a FASTA file
reverse Reverse sequences
rev_comp Revere complement sequences
write_greengenes Write an imitation of the Greengenes database
write_mothur_taxonomy Write an imitation of the Mothur taxonomy file
write_rdp Write an imitation of the RDP FASTA database
write_silva_fasta Write an imitation of the SILVA FASTA database
write_unite_general Write an imitation of the UNITE general FASTA database
zero_low_counts Replace low counts with zero