Package: LocaTT 1.1.15

LocaTT: Geographically-Conscious Taxonomic Assignment for Metabarcoding

A bioinformatics pipeline for performing taxonomic assignment of DNA metabarcoding sequence data while considering geographic location. A detailed tutorial is available at <https://urodelan.github.io/Local_Taxa_Tool_Tutorial/>. A manuscript describing these methods is in preparation.

Authors:Kenen Goodwin [aut, cre], Taal Levi [aut]

LocaTT_1.1.15.tar.gz
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LocaTT.pdf |LocaTT.html✨
LocaTT/json (API)

Peer review:

Bug tracker:https://github.com/urodelan/locatt/issues

On CRAN:

28 exports 1.30 score 123 dependencies 1 scripts 806 downloads

Last updated 6 months agofrom:90985b382b. Checks:OK: 7. Indexed: yes.

Exports:adjust_taxonomiesbinomial_testblast_command_foundblast_versioncontains_wildcardsdecode_quality_scoresexpand_taxonomiesfilter_sequencesformat_reference_databaseget_consensus_taxonomyget_taxonomic_levelget_taxonomies.IUCNget_taxonomies.species_binomialsisolate_ampliconlocal_taxa_toolmerge_pairsread.fastaread.fastqreverse_complementsubstitute_wildcardssummarize_quality_scorestrim_sequencestruncate_and_merge_pairstruncate_sequences.lengthtruncate_sequences.probabilitytruncate_sequences.quality_scorewrite.fastawrite.fastq

Dependencies:apeaskpassassertthatbackportsbase64encbitbit64boldbslibcachemcheckmateclicliprclustercodetoolscolorspaceconditionzcpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplyphangornpillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessolriumstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8uuidvctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo