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_1.1.15.tgz(r-4.4-any)LocaTT_1.1.15.tgz(r-4.3-any)
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LocaTT.pdf |LocaTT.html✨
LocaTT/json (API)

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

Peer review:

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

On CRAN:

3.18 score 1 scripts 577 downloads 28 exports 122 dependencies

Last updated 8 months agofrom:90985b382b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winOKSep 20 2024
R-4.5-linuxOKNov 01 2024
R-4.4-winOKSep 20 2024
R-4.4-macOKSep 20 2024
R-4.3-winOKSep 20 2024
R-4.3-macOKSep 20 2024

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:apeaskpassassertthatbackportsbase64encbitbit64bslibcachemcheckmateclicliprclustercodetoolscolorspaceconditionzcpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplyphangornpillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessolriumstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8uuidvctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo

Readme and manuals

Help Manual

Help pageTopics
Adjust Taxonomiesadjust_taxonomies
Binomial Testbinomial_test
Check BLAST Installationblast_command_found
Get BLAST Versionblast_version
Check Whether DNA Sequences Contain Wildcard Characterscontains_wildcards
Decode DNA Sequence Quality Scoresdecode_quality_scores
Expand Taxonomiesexpand_taxonomies
Filter DNA Sequences by PCR Replicatesfilter_sequences
Format Reference Databasesformat_reference_database
Get Consensus Taxonomy from Taxonomic Stringsget_consensus_taxonomy
Get Specified Taxonomic Level from Taxonomic Stringsget_taxonomic_level
Get Taxonomies from IUCN Red List Filesget_taxonomies.IUCN
Get NCBI Taxonomies from Species Binomialsget_taxonomies.species_binomials
Trim DNA Sequences to an Amplicon Region Using Forward and Reverse Primer Sequencesisolate_amplicon
Perform Geographically-Conscious Taxonomic Assignmentlocal_taxa_tool
Merge Forward and Reverse DNA Sequence Readsmerge_pairs
Read FASTA Filesread.fasta
Read FASTQ Filesread.fastq
Get the Reverse Complement of a DNA Sequencereverse_complement
Substitute Wildcard Characters in a DNA Sequencesubstitute_wildcards
Summarize Quality Scoressummarize_quality_scores
Trim Target Nucleotide Sequence from DNA Sequencestrim_sequences
Truncate and Merge Forward and Reverse DNA Sequence Readstruncate_and_merge_pairs
Truncate DNA Sequences to Specified Lengthtruncate_sequences.length
Truncate DNA Sequences at Specified Probability that All Bases were Called Correctlytruncate_sequences.probability
Truncate DNA Sequences at Specified Quality Scoretruncate_sequences.quality_score
Write FASTA Fileswrite.fasta
Write FASTQ Fileswrite.fastq