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
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manual.pdf |manual.html✨
DESCRIPTION
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.

sequencing dataimport

3.30 score 1 mentions 36 exports 50 dependencies

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

Target	Result	Time
bioc-checks	ERROR	174
linux-devel-x86_64	NOTE	356
source / vignettes	OK	235
linux-release-x86_64	NOTE	309
macos-release-arm64	NOTE	175
macos-oldrel-arm64	NOTE	153
windows-devel	NOTE	249
windows-release	NOTE	231
windows-oldrel	NOTE	241
wasm-release	OK	169

Exports:abundance aData aData<-assignmentData assignmentData<-assignmentLabels assignmentLabels<-assignmentNames clusterSamples getOTUs getSamples notus nsamples o_diversity o_estimateR otuID otuseqplot otusize otuspersample readOTUset readTAXset rseqplot sampleData sampleData<-sampleID sampleLabels sampleLabels<-sData sData<-seqnames seqspersample sharedotus subOTUset subTAXset tax tax<-

Dependencies:abind BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo cluster codetools cpp11 crayon DelayedArray deldir formatR futile.logger futile.options generics GenomicAlignments GenomicRanges hwriter interp IRanges jpeg lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats mgcv nlme permute png pwalign RColorBrewer Rcpp RcppEigen Rhtslib Rsamtools S4Arrays S4Vectors Seqinfo ShortRead snow SparseArray SummarizedExperiment vegan XVector

An introduction to OTUbase

A simple workflow | Advanced features | The structure of an OTUbase object | Conclusions and directions for development | References

Rendered fromIntroduction_to_OTUbase.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The OTUbase package: A tool for organizing and manipulating Operational Taxonomic Unit data	OTUbase-package OTUbase
"OTUset" class for OTU data	OTUset OTUsetB OTUsetB-class OTUsetF OTUsetF-class OTUsetQ OTUsetQ-class
"TAXset" class for TAX data	TAXset TAXsetB TAXsetB-class TAXsetF TAXsetF-class TAXsetQ TAXsetQ-class
abundance	abundance abundance,.OTUset-method abundance,.TAXset-method
Accessor functions for OTUset and TAXset objects	otuID otuID,.OTUset-method sampleID sampleID,.OTUbase-method tax tax,.TAXset-method tax<- tax<-,.TAXset,data.frame-method tax<-,.TAXset-method
assignmentData	aData 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
clusterSamples	clusterSamples clusterSamples,.OTUset-method clusterSamples,.TAXset-method clusterSamples-generic clusterSamples-method
Other functions	getOTUs getSamples otuseqplot otusize otuspersample o_diversity o_estimateR rseqplot seqspersample sharedotus
Other Generics	notus notus,.OTUset-method nsamples nsamples,.OTUbase-method seqnames seqnames,.OTUbase-method
readOTUset	readOTUset
readTAXset	readTAXset
sampleData	sampleData 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
subOTUset	subOTUset
subTAXset	subTAXset