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

Provides a platform for Operational Taxonomic Unit based analysis

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("OTUbase")
AuthorDaniel Beck, Matt Settles, and James A. Foster
Bioconductor views DataImport Sequencing
Date of publicationNone
MaintainerDaniel Beck <danlbek@gmail.com>
LicenseArtistic-2.0
Version1.24.0

View on Bioconductor

Functions

abundance Man page
abundance,.OTUset-method Man page
abundance,.TAXset-method Man page
aData Man page
aData<- Man page
aData<-,.OTUbase,data.frame-method Man page
aData<-,.OTUbase-method Man page
aData,.OTUbase-method Man page
assignmentData Man page
assignmentData<- Man page
assignmentData<-,.OTUbase,AnnotatedDataFrame-method Man page
assignmentData<-,.OTUbase-method Man page
assignmentData,.OTUbase-method Man page
assignmentLabels Man page
assignmentLabels<- Man page
assignmentLabels<-,.OTUbase,character-method Man page
assignmentLabels<-,.OTUbase-method Man page
assignmentLabels,.OTUbase-method Man page
assignmentNames Man page
assignmentNames,.OTUbase-method Man page
clusterSamples Man page
clusterSamples-generic Man page
clusterSamples-method Man page
clusterSamples,.OTUset-method Man page
clusterSamples,.TAXset-method Man page
getOTUs Man page
getSamples Man page
notus Man page
notus,.OTUset-method Man page
nsamples Man page
nsamples,.OTUbase-method Man page
o_diversity Man page
o_estimateR Man page
OTUbase Man page
OTUbase-package Man page
otuID Man page
otuID,.OTUset-method Man page
otuseqplot Man page
OTUset Man page
OTUsetB Man page
OTUsetB-class Man page
OTUsetF Man page
OTUsetF-class Man page
OTUsetQ Man page
OTUsetQ-class Man page
otusize Man page
otuspersample Man page
readOTUset Man page
readTAXset Man page
rseqplot Man page
sampleData Man page
sampleData<- Man page
sampleData<-,.OTUbase,AnnotatedDataFrame-method Man page
sampleData<-,.OTUbase-method Man page
sampleData,.OTUbase-method Man page
sampleID Man page
sampleID,.OTUbase-method Man page
sampleLabels Man page
sampleLabels<- Man page
sampleLabels<-,.OTUbase,character-method Man page
sampleLabels<-,.OTUbase-method Man page
sampleLabels,.OTUbase-method Man page
sData Man page
sData<- Man page
sData<-,.OTUbase,data.frame-method Man page
sData<-,.OTUbase-method Man page
sData,.OTUbase-method Man page
seqnames Man page
seqnames,.OTUbase-method Man page
seqspersample Man page
sharedotus Man page
subOTUset Man page
subTAXset Man page
tax Man page
tax<- Man page
TAXset Man page
TAXsetB Man page
TAXsetB-class Man page
TAXsetF Man page
TAXsetF-class Man page
TAXsetQ Man page
TAXsetQ-class Man page
tax<-,.TAXset,data.frame-method Man page
tax<-,.TAXset-method Man page
tax,.TAXset-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/methods-OTUbase.R R/methods-OTUset.R R/methods-TAXset.R R/utils-general.R R/utils-summary.R R/utils-tax.R R/zzz.R
build
build/vignette.rds
inst
inst/doc
inst/doc/Introduction_to_OTUbase.R
inst/doc/Introduction_to_OTUbase.Rnw
inst/doc/Introduction_to_OTUbase.pdf
inst/extdata
inst/extdata/Sogin_2006
inst/extdata/Sogin_2006/sample_metadata.txt
inst/extdata/Sogin_2006/sogin.fasta
inst/extdata/Sogin_2006/sogin.groups
inst/extdata/Sogin_2006/sogin.names
inst/extdata/Sogin_2006/sogin.rep.fix.tax
inst/extdata/Sogin_2006/sogin.unique.filter.fn.0.03.rep.fasta
inst/extdata/Sogin_2006/sogin.unique.filter.fn.list
inst/extdata/Sogin_2006/sogin.unique.fix.tax
man
man/OTUbase-package.Rd man/OTUset-class.Rd man/TAXset-class.Rd man/abundance.Rd man/accessors.Rd man/assignmentData.Rd man/clusterSamples.Rd man/other_functions.Rd man/other_generics.Rd man/readOTUset.Rd man/readTAXset.Rd man/sampleData.Rd man/subOTUset.Rd man/subTAXset.Rd
vignettes
vignettes/Introduction_to_OTUbase.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.