Package: metacoder 0.3.8
metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.
Authors:
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NEWS
# Install 'metacoder' in R: |
install.packages('metacoder', repos = c('https://grunwaldlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/grunwaldlab/metacoder/issues
- ex_taxmap - An example taxmap object
- hmp_otus - A HMP subset
- hmp_samples - Sample information for HMP subset
- ranks_ref - Lookup-table for IDs of taxonomic ranks
community-diversityhierarchicalmetabarcodingpcrtaxonomytreescpp
Last updated 5 days agofrom:e881d1bc67. Checks:1 OK, 10 NOTE. Indexed: yes.
Target | Result | Latest binary |
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Doc / Vignettes | OK | Feb 12 2025 |
R-4.5-win-x86_64 | NOTE | Feb 12 2025 |
R-4.5-mac-x86_64 | NOTE | Feb 12 2025 |
R-4.5-mac-aarch64 | NOTE | Feb 12 2025 |
R-4.5-linux-x86_64 | NOTE | Feb 12 2025 |
R-4.4-win-x86_64 | NOTE | Feb 12 2025 |
R-4.4-mac-x86_64 | NOTE | Feb 12 2025 |
R-4.4-mac-aarch64 | NOTE | Feb 12 2025 |
R-4.3-win-x86_64 | NOTE | Feb 12 2025 |
R-4.3-mac-x86_64 | NOTE | Feb 12 2025 |
R-4.3-mac-aarch64 | NOTE | Feb 12 2025 |
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:ade4apeaskpassassertthatbackportsbase64encbitbit64bitopsbslibcachemcheckmateclicliprclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsGAgenericsggfittextggplot2gluegridExtragridtextgtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjpegjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrmarkdownMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplypermutephangornpillarpixmappkgconfigplyrpngprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppRcppArmadilloRCurlreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessegmentedseqinrshadessolriumspstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8vctrsveganviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo