Package: metacoder 0.3.7

Zachary Foster

metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).

Authors:Zachary Foster [aut, cre], Niklaus Grunwald [ths], Rob Gilmore [ctb]

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NEWS

# Install 'metacoder' in R:
install.packages('metacoder', repos = c('https://grunwaldlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/grunwaldlab/metacoder/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

community-diversityhierarchicalmetabarcodingpcrtaxonomytrees

9.17 score 135 stars 314 scripts 515 downloads 32 mentions 128 exports 141 dependencies

Last updated 9 months agofrom:54ef8eabc5. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 17 2024
R-4.5-win-x86_64NOTESep 17 2024
R-4.5-linux-x86_64NOTEOct 17 2024
R-4.4-win-x86_64NOTESep 17 2024
R-4.4-mac-x86_64NOTESep 17 2024
R-4.4-mac-aarch64NOTESep 17 2024
R-4.3-win-x86_64NOTESep 17 2024
R-4.3-mac-x86_64NOTESep 17 2024
R-4.3-mac-aarch64NOTESep 17 2024

Exports:%>%all_namesambiguous_synonymsarrange_obsarrange_taxaas_phyloseqbranchescalc_diff_abund_deseq2calc_group_meancalc_group_mediancalc_group_rsdcalc_group_statcalc_n_samplescalc_obs_propscalc_prop_samplescalc_taxon_abundclassificationscompare_groupscomplementcontainscounts_to_presencedatabase_listdiverging_paletteends_witheverythingextract_tax_datafilter_ambiguous_taxafilter_obsfilter_taxaget_dataget_data_frameget_datasetheat_treeheat_tree_matrixhierarchieshierarchyid_classificationsidsinternodesis_ambiguousis_branchis_internodeis_leafis_rootis_stemlayout_functionsleavesleaves_applylookup_tax_datamake_dada2_asv_tablemake_dada2_tax_tablemap_datamap_data_matchesmutate_obsn_leavesn_leaves_1n_obsn_obs_1n_subtaxan_subtaxa_1n_supertaxan_supertaxa_1ncbi_taxon_samplenmsnum_rangeobsobs_applyone_ofparse_dada2parse_edge_listparse_greengenesparse_mothur_tax_summaryparse_mothur_taxonomyparse_newickparse_phyloparse_phyloseqparse_primersearchparse_qiime_biomparse_rdpparse_silva_fastaparse_tax_dataparse_ubiomeparse_unite_generalprimersearchprimersearch_rawprint_treequalitative_palettequantative_paletteranksrarefy_obsread_fastaremove_redundant_namesreplace_taxon_idsrev_compreverserootssample_frac_obssample_frac_taxasample_n_obssample_n_taxaselect_obsstarts_withstemssubtaxasubtaxa_applysupertaxasupertaxa_applytaxataxmaptaxontaxon_databasetaxon_idtaxon_idstaxon_indexestaxon_nametaxon_namestaxon_ranktaxon_rankstaxonomytaxonomy_tabletransmute_obswrite_greengeneswrite_mothur_taxonomywrite_rdpwrite_silva_fastawrite_unite_generalzero_low_counts

Dependencies:ade4apeaskpassassertthatbackportsbase64encbitbit64bitopsbslibcachemcheckmateclicliprclustercodetoolscolorspacecommonmarkconditionzcowplotcpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsGAgenericsggfittextggplot2gluegridExtragridtextgtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjpegjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrmarkdownMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplypermutephangornpillarpixmappkgconfigplyrpngprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppRcppArmadilloRCurlreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessegmentedseqinrshadessolriumspstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8uuidvctrsveganviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo

Documentation for metacoder

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Oct 17 2024.

Last update: 2021-06-23
Started: 2016-04-11

Readme and manuals

Help Manual

Help pageTopics
Return names of data in [taxonomy()] or [taxmap()]all_names
Get patterns for ambiguous taxaambiguous_synonyms
Sort user data in [taxmap()] objectsarrange_obs
Sort the edge list of [taxmap()] objectsarrange_taxa
Convert taxmap to phyloseqas_phyloseq
Get "branch" taxabranches
Differential abundance with DESeq2calc_diff_abund_deseq2
Calculate means of groups of columnscalc_group_mean
Calculate medians of groups of columnscalc_group_median
Relative standard deviations of groups of columnscalc_group_rsd
Apply a function to groups of columnscalc_group_stat
Count the number of samplescalc_n_samples
Calculate proportions from observation countscalc_obs_props
Calculate the proportion of samplescalc_prop_samples
Get classifications of taxaclassifications
Compare groups of samplescompare_groups
Find complement of sequencescomplement
Apply a function to groups of columnscounts_to_presence
Database listdatabase_list
The default diverging color palettediverging_palette
An example hierarchies objectex_hierarchies
An example Hierarchy objectex_hierarchy1
An example Hierarchy objectex_hierarchy2
An example Hierarchy objectex_hierarchy3
An example taxmap objectex_taxmap
Extracts taxonomy info from vectors with regexextract_tax_data
Filter ambiguous taxon namesfilter_ambiguous_taxa
Filter observations with a list of conditionsfilter_obs
Filter taxa with a list of conditionsfilter_taxa
Taxonomic filtering helpersfiltering-helpers ids nms ranks
Get data in a taxmap object by nameget_data
Get data in a taxonomy or taxmap object by nameget_data_frame
Get a data set from a taxmap objectget_dataset
Plot a taxonomic treeheat_tree heat_tree.default heat_tree.Taxmap
Plot a matrix of heat treesheat_tree_matrix
Make a set of many [hierarchy()] class objectshierarchies
The Hierarchy classhierarchy
Highlight taxon ID columnhighlight_taxon_ids
A HMP subsethmp_otus
Sample information for HMP subsethmp_samples
Get ID classifications of taxaid_classifications
Get "internode" taxainternodes
Find ambiguous taxon namesis_ambiguous
Test if taxa are branchesis_branch
Test if taxa are "internodes"is_internode
Test if taxa are leavesis_leaf
Test if taxa are rootsis_root
Test if taxa are stemsis_stem
Layout functionslayout_functions
Get leaf taxaleaves
Apply function to leaves of each taxonleaves_apply
Convert one or more data sets to taxmaplookup_tax_data
Make a imitation of the dada2 ASV abundance matrixmake_dada2_asv_table
Make a imitation of the dada2 taxonomy matrixmake_dada2_tax_table
Create a mapping between two variablesmap_data
Create a mapping without NSEmap_data_
Metacodermetacoder
Add columns to [taxmap()] objectsmutate_obs
Get number of leavesn_leaves
Get number of leavesn_leaves_1
Count observations in [taxmap()]n_obs
Count observation assigned in [taxmap()]n_obs_1
Get number of subtaxan_subtaxa
Get number of subtaxan_subtaxa_1
Get number of supertaxan_supertaxa
Get number of supertaxan_supertaxa_1
Download representative sequences for a taxonncbi_taxon_sample
Get data indexes associated with taxaobs
Apply function to observations per taxonobs_apply
Convert the output of dada2 to a taxmap objectparse_dada2
Parse Greengenes releaseparse_greengenes
Parse mothur *.tax.summary Classify.seqs outputparse_mothur_tax_summary
Parse mothur Classify.seqs *.taxonomy outputparse_mothur_taxonomy
Parse a Newick fileparse_newick
Parse a phylo objectparse_phylo
Convert a phyloseq to taxmapparse_phyloseq
Parse EMBOSS primersearch outputparse_primersearch
Parse a BIOM output from QIIMEparse_qiime_biom
Parse RDP FASTA releaseparse_rdp
Parse SILVA FASTA releaseparse_silva_fasta
Convert one or more data sets to taxmapparse_tax_data
Converts the uBiome file format to taxmapparse_ubiome
Parse UNITE general release FASTAparse_unite_general
Use EMBOSS primersearch for in silico PCRprimersearch
Use EMBOSS primersearch for in silico PCRprimersearch_raw
Print a text treeprint_tree
The default qualitative color palettequalitative_palette
The default quantative color palettequantative_palette
Lookup-table for IDs of taxonomic ranksranks_ref
Calculate rarefied observation countsrarefy_obs
Read a FASTA fileread_fasta
Remove redundant parts of taxon namesremove_redundant_names
Replace taxon idsreplace_taxon_ids
Revere complement sequencesrev_comp
Reverse sequencesreverse
Get root taxaroots
Sample a proportion of observations from [taxmap()]sample_frac_obs
Sample a proportion of taxa from [taxonomy()] or [taxmap()]sample_frac_taxa
Sample n observations from [taxmap()]sample_n_obs
Sample n taxa from [taxonomy()] or [taxmap()]sample_n_taxa
Subset columns in a [taxmap()] objectselect_obs
Get stem taxastems
Get subtaxasubtaxa
Apply function to subtaxa of each taxonsubtaxa_apply
Get all supertaxa of a taxonsupertaxa
Apply function to supertaxa of each taxonsupertaxa_apply
A class for multiple taxon objectstaxa
Taxmap classtaxmap
Taxon classtaxon
Taxonomy database classtaxon_database
Taxon ID classtaxon_id
Get taxon IDstaxon_ids
Get taxon indexestaxon_indexes
Taxon name classtaxon_name
Get taxon namestaxon_names
Taxon rank classtaxon_rank
Get taxon rankstaxon_ranks
Taxonomy classtaxonomy
Convert taxonomy info to a tabletaxonomy_table
Replace columns in [taxmap()] objectstransmute_obs
Write an imitation of the Greengenes databasewrite_greengenes
Write an imitation of the Mothur taxonomy filewrite_mothur_taxonomy
Write an imitation of the RDP FASTA databasewrite_rdp
Write an imitation of the SILVA FASTA databasewrite_silva_fasta
Write an imitation of the UNITE general FASTA databasewrite_unite_general
Replace low counts with zerozero_low_counts