Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data


[Up] [Top]

Documentation for package ‘metacoder’ version 0.2.0

Help Pages

metacoder-package Metacoder
calc_n_samples Count the number of samples
calc_obs_props Calculate proportions from observation counts
calc_taxon_abund Sum observation values for each taxon
compare_groups Compare groups of samples
complement Find complement of sequences
diverging_palette The default diverging color palette
filter_ambiguous_taxa Filter ambiguous taxon names
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
metacoder Metacoder
ncbi_taxon_sample Download representative sequences for a taxon
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_unite_general Parse UNITE general release FASTA
primersearch 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 databse
write_mothur_taxonomy Write an imitation of the Mothur taxonomy file
write_rdp Write an imitation of the RDP FASTA databse
write_silva_fasta Write an imitation of the SILVA FASTA databse
write_unite_general Write an imitation of the UNITE general FASTA databse
zero_low_counts Replace low counts with zero