Package: OTUbase 1.63.0

Daniel Beck

OTUbase: Provides structure and functions for the analysis of OTU data

Provides a platform for Operational Taxonomic Unit based analysis

Authors:Daniel Beck, Matt Settles, and James A. Foster

OTUbase_1.63.0.tar.gz
OTUbase_1.63.0.zip(r-4.7)OTUbase_1.63.0.zip(r-4.6)OTUbase_1.63.0.zip(r-4.5)
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OTUbase_1.63.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OTUbase/json (API)

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

On BioConductor:OTUbase-1.63.0(bioc 3.24)OTUbase-1.62.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencingdataimport

3.30 score 3 scripts 442 downloads 1 mentions 36 exports 50 dependencies

Last updated from:638fb2e6f6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR176
linux-devel-x86_64NOTE326
source / vignettesOK257
linux-release-x86_64NOTE410
macos-release-arm64NOTE162
macos-oldrel-arm64NOTE195
windows-develNOTE241
windows-releaseNOTE245
windows-oldrelNOTE261
wasm-releaseOK146

Exports:abundanceaDataaData<-assignmentDataassignmentData<-assignmentLabelsassignmentLabels<-assignmentNamesclusterSamplesgetOTUsgetSamplesnotusnsampleso_diversityo_estimateRotuIDotuseqplototusizeotuspersamplereadOTUsetreadTAXsetrseqplotsampleDatasampleData<-sampleIDsampleLabelssampleLabels<-sDatasData<-seqnamesseqspersamplesharedotussubOTUsetsubTAXsettaxtax<-

Dependencies:abindBHBiobaseBiocGenericsBiocParallelBiostringsbitopscigarilloclustercodetoolscpp11crayonDelayedArraydeldirformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangeshwriterinterpIRangesjpeglambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatsmgcvnlmepermutepngpwalignRColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsSeqinfoShortReadsnowSparseArraySummarizedExperimentveganXVector

An introduction to OTUbase

Rendered fromIntroduction_to_OTUbase.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2020-06-07
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
The OTUbase package: A tool for organizing and manipulating Operational Taxonomic Unit dataOTUbase-package OTUbase
"OTUset" class for OTU dataOTUset OTUsetB OTUsetB-class OTUsetF OTUsetF-class OTUsetQ OTUsetQ-class
"TAXset" class for TAX dataTAXset TAXsetB TAXsetB-class TAXsetF TAXsetF-class TAXsetQ TAXsetQ-class
abundanceabundance abundance,.OTUset-method abundance,.TAXset-method
Accessor functions for OTUset and TAXset objectsotuID otuID,.OTUset-method sampleID sampleID,.OTUbase-method tax tax,.TAXset-method tax<- tax<-,.TAXset,data.frame-method tax<-,.TAXset-method
assignmentDataaData aData,.OTUbase-method aData<- aData<-,.OTUbase,data.frame-method aData<-,.OTUbase-method assignmentData assignmentData,.OTUbase-method assignmentData<- assignmentData<-,.OTUbase,AnnotatedDataFrame-method assignmentData<-,.OTUbase-method assignmentLabels assignmentLabels,.OTUbase-method assignmentLabels<- assignmentLabels<-,.OTUbase,character-method assignmentLabels<-,.OTUbase-method assignmentNames assignmentNames,.OTUbase-method
clusterSamplesclusterSamples clusterSamples,.OTUset-method clusterSamples,.TAXset-method clusterSamples-generic clusterSamples-method
Other functionsgetOTUs getSamples otuseqplot otusize otuspersample o_diversity o_estimateR rseqplot seqspersample sharedotus
Other Genericsnotus notus,.OTUset-method nsamples nsamples,.OTUbase-method seqnames seqnames,.OTUbase-method
readOTUsetreadOTUset
readTAXsetreadTAXset
sampleDatasampleData sampleData,.OTUbase-method sampleData<- sampleData<-,.OTUbase,AnnotatedDataFrame-method sampleData<-,.OTUbase-method sampleLabels sampleLabels,.OTUbase-method sampleLabels<- sampleLabels<-,.OTUbase,character-method sampleLabels<-,.OTUbase-method sData sData,.OTUbase-method sData<- sData<-,.OTUbase,data.frame-method sData<-,.OTUbase-method
subOTUsetsubOTUset
subTAXsetsubTAXset