microclass: Methods for Taxonomic Classification of Prokaryotes
Version 1.1

Functions for assigning 16S sequence data to a taxonomic level in the tree-of-life for prokaryotes.

Browse man pages Browse package API and functions Browse package files

AuthorKristian Hovde Liland, Hilde Vinje, Lars Snipen
Date of publication2017-01-17 19:41:20
MaintainerLars Snipen <lars.snipen@nmbu.no>
LicenseGPL (>= 2)
Version1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("microclass")

Man pages

blastClassify16S: Classifying using BLAST
blastDbase16S: Building a BLAST database
KmerCount: K-mer counting
microclass-package: Methods for 16S based taxonomic classification of prokaryotes
multinomClassify: Classifying with a Multinomial model
multinomTrain: Training multinomial model
rdpClassify: Classifying with the RDP classifier
rdpTrain: Training the RDP classifier
setParallel: Set number of parallel threads
small.16S: A small example data set
taxMachine: Classifying 16S sequences

Functions

CountsToMultinom Source code
CountsToMultinomMulti Source code
CountsToRDP Source code
KmerCount Man page Source code
Kmer_count Source code
blastClassify16S Man page Source code
blastDbase16S Man page Source code
charToInt Source code
getmicroEnv Source code
microEnv Source code
microclass Man page Source code
microclass-package Man page
multinomClassify Man page Source code
multinomClassifyCpp Source code
multinomTrain Man page Source code
multinomTrainCpp Source code
putmicroEnv Source code
rdpClassify Man page Source code
rdpClassifyCpp Source code
rdpTrain Man page Source code
rdpTrainCpp Source code
setParallel Man page Source code
small.16S Man page
taxMachine Man page Source code

Files

inst
inst/extdata
inst/extdata/rprob.mat.1400.rda
inst/extdata/std.frame.rda
inst/extdata/norm.models.rda
inst/extdata/rprob.mat.500.rda
inst/extdata/rprob.mat.300.rda
inst/extdata/rprob.mat.150.rda
inst/doc
inst/doc/intro.html
inst/doc/intro.R
inst/doc/intro.Rmd
src
src/rdpTrainCpp.cpp
src/Makevars
src/pow4int.cpp
src/charToInt.cpp
src/multinomTrainCpp.cpp
src/pow4inthead.h
src/KmerCount.cpp
src/Makevars.win
src/rdpClassifyCpp.cpp
src/RcppExports.cpp
src/multinomClassify.cpp
NAMESPACE
data
data/small.16S.rda
R
R/taxMachine.R
R/multinom.R
R/RcppExports.R
R/blast.R
R/rdpClassifier.R
R/KmerCount.R
R/datasets.R
R/zzz.R
R/microclass-package.R
vignettes
vignettes/intro.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/rdpClassify.Rd
man/rdpTrain.Rd
man/multinomTrain.Rd
man/microclass-package.Rd
man/multinomClassify.Rd
man/KmerCount.Rd
man/blastClassify16S.Rd
man/small.16S.Rd
man/blastDbase16S.Rd
man/setParallel.Rd
man/taxMachine.Rd
microclass documentation built on May 19, 2017, 8:47 p.m.