Package: OTUbase 1.57.0

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

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OTUbase.pdf |OTUbase.html✨
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-1.55.0(bioc 3.20)OTUbase-1.54.0(bioc 3.19)

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 254 downloads 1 mentions 36 exports 59 dependencies

Last updated 23 days agofrom:4de67742c6. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

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 askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops cluster codetools cpp11 crayon curl DelayedArray deldir formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges httr hwriter interp IRanges jpeg jsonlite lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats mgcv mime nlme openssl permute png pwalign R6 RColorBrewer Rcpp RcppEigen Rhtslib Rsamtools S4Arrays S4Vectors ShortRead snow SparseArray SummarizedExperiment sys UCSC.utils vegan XVector zlibbioc

An introduction to OTUbase

Rendered fromIntroduction_to_OTUbase.Rnwusingutils::Sweaveon Oct 30 2024.

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