metacoder-package | Metacoder |
arrange_obs | Sort columns of 'taxmap' objects |
arrange_taxa | Sort columns of 'taxmap' objects |
bryophytes_ex_data | Example dataset of bryophytes |
contaminants | Example dataset of comtamination |
diverging_palette | The defualt diverging color palette |
extract_taxonomy | Extract taxonomy information from sequence headers |
extract_taxonomy.default | Extract taxonomy information from sequence headers |
extract_taxonomy.DNAbin | Extract taxonomy information from sequence headers |
extract_taxonomy.list | Extract taxonomy information from sequence headers |
filter_obs | Filter observations with a list of conditions |
filter_taxa | Filter taxa with a list of conditions |
genbank_ex_data | Fungal ITS Genbank refseq |
hierarchies | Get classification of taxa |
its1_ex_data | Example of ITS1 fungal data |
layout_functions | Layout functions |
metacoder | Metacoder |
mutate_obs | Add columns to 'taxmap' objects |
mutate_taxa | Add columns to 'taxmap' objects |
n_obs | Count observations in 'taxmap' |
n_obs_1 | Count observation assigned in 'taxmap' |
n_subtaxa | Get number of subtaxa |
n_subtaxa_1 | Get number of subtaxa |
n_supertaxa | Get number of supertaxa |
obs | Get observations associated with taxa |
obs_data | Return observation data from 'taxmap' |
obs_data_colnames | Get column names of obs_data |
parse_hmp_qiime | Parse HMP QIIME results |
parse_mothur_summary | Parse mothur classification summary file |
parse_taxonomy_table | Parse taxonomic data in a tsv/csv file |
pr2_ex_data | Example of PR2 SSU data |
primersearch | Use EMBOSS primersearch for in silico PCR |
primersearch.character | Use EMBOSS primersearch for in silico PCR |
primersearch.taxmap | Use EMBOSS primersearch for in silico PCR |
print.taxmap | Print a 'taxmap' object |
qualitative_palette | The defualt qualitative color palette |
quantative_palette | The defualt quantative color palette |
rdp_ex_data | Example of RDP Archea data |
read_fasta | Read a FASTA file |
remove_redundant_names | Remove the redundant taxon names |
roots | Get root taxa |
sample_frac_obs | Sample a proportion of observations from 'taxmap' |
sample_frac_taxa | Sample a proportion of taxa from 'taxmap' |
sample_n_obs | Sample n observations from 'taxmap' |
sample_n_taxa | Sample n taxa from 'taxmap' |
select_obs | Subset columns in a 'taxmap' object |
select_taxa | Subset columns in a 'taxmap' object |
silva_ex_data | Example dataset from SILVA |
subtaxa | Get all subtaxa of a taxon |
supertaxa | Get all supertaxa of a taxon |
taxmap | Create an instance of 'taxmap' |
taxonomic_sample | Recursivly sample a set of taxonomic assignments |
taxon_data | Return taxon data from 'taxmap' |
taxon_data_colnames | Get column names of taxon_data |
transmute_obs | Replace columns in 'taxmap' objects |
transmute_taxa | Replace columns in 'taxmap' objects |
unite_ex_data_1 | Example of UNITE fungal ITS data |
unite_ex_data_2 | Example of UNITE fungal ITS data |
unite_ex_data_3 | Example of UNITE fungal ITS data |