# Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

## Documentation for package ‘metacoder’ version 0.3.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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