Package: LocaTT 1.2.7

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/LocaTT_Tutorial/>. A manuscript describing these methods is in preparation.

Authors:Kenen B Goodwin [aut, cre], Christopher Cousins [ctb], Taal Levi [ctb], Tiffany S Garcia [ths]

LocaTT_1.2.7.tar.gz
LocaTT_1.2.7.zip(r-4.7)LocaTT_1.2.7.zip(r-4.6)LocaTT_1.2.7.zip(r-4.5)
LocaTT_1.2.7.tgz(r-4.6-any)LocaTT_1.2.7.tgz(r-4.5-any)
LocaTT_1.2.7.tar.gz(r-4.7-any)LocaTT_1.2.7.tar.gz(r-4.6-any)
LocaTT_1.2.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
LocaTT/json (API)

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

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

On CRAN:

Conda:

3.65 score 2 scripts 631 downloads 56 exports 0 dependencies

Last updated from:65246c6454. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK153
source / vignettesOK169
linux-release-x86_64OK154
macos-release-arm64OK137
macos-oldrel-arm64OK169
windows-develOK164
windows-releaseOK118
windows-oldrelOK447
wasm-releaseOK119

Exports:adjust_taxonomiesbinomial_testblast_command_foundblast_versioncirclecontains_wildcardscoordinatescor2covdcopuladdirmultdecode_quality_scoresdetectiondissimilaritydiversitydjsdmdmpredictdmregdmvlogisdmWAICexpand_taxonomiesfilter_sequencesformat_reference_databaseget_consensus_taxonomyget_taxonomic_levelget_taxonomies.IUCNget_taxonomies.species_binomialsisolate_ampliconlocal_taxa_toolmerge_pairsmlcoefmlcormlformatmlpredictmlregmlWAICnormalizeproportionread.fastaread.fastqreverse_complementrichnesssectorsingular.detectionsingular.proportionsoftmaxsubstitute_wildcardssummarize_quality_scorestemplatetrim_sequencestruncate_and_merge_pairstruncate_sequences.lengthtruncate_sequences.probabilitytruncate_sequences.quality_scorewaicwrite.fastawrite.fastq

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Adjust Taxonomiesadjust_taxonomies
Binomial Testbinomial_test
Check BLAST Installationblast_command_found
Get BLAST Versionblast_version
Draw Circle Polygoncircle
Check Whether DNA Sequences Contain Wildcard Characterscontains_wildcards
Generate Circular Coordinatescoordinates
Convert Correlation to Covariance Matrixcor2cov
Density of the Gaussian Copuladcopula
Density of the Dirichlet-Multinomial Distributionddirmult
Decode DNA Sequence Quality Scoresdecode_quality_scores
Grouped Detection Plotdetection
Bray-Curtis Dissimilarity (Proportion Form)dissimilarity
Hill Diversitydiversity
Density of a Joint Species Distribution Modeldjsdm
Predictions for Dirichlet-Multinomial Regression Modelsdmpredict
Fitting Dirichlet-Multinomial Regression Modelsdmreg
Density of the Multivariate Logistic Distributiondmvlogis
WAIC for Dirichlet-Multinomial Regression ModelsdmWAIC
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
Coefficients of Multivariate Logistic Regression Modelsmlcoef
Correlations of Multivariate Logistic Regression Modelsmlcor
Formatting Multivariate Logistic Regression Outputmlformat
Predictions for Multivariate Logistic Regression Modelsmlpredict
Fitting Multivariate Logistic Regression Modelsmlreg
WAIC for Multivariate Logistic Regression ModelsmlWAIC
Normalize a Vector or Matrixnormalize
Grouped Proportion Plotproportion
Read FASTA Filesread.fasta
Read FASTQ Filesread.fastq
Get the Reverse Complement of a DNA Sequencereverse_complement
Species Richnessrichness
Draw Sector Polygonsector
Singular Detection Plotsingular.detection
Singular Proportion Plotsingular.proportion
The Softmaxsoftmax
Substitute Wildcard Characters in a DNA Sequencesubstitute_wildcards
Summarize Quality Scoressummarize_quality_scores
Initiate Template Plottemplate
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
Widely Applicable Information Criterionwaic
Write FASTA Fileswrite.fasta
Write FASTQ Fileswrite.fastq