microclass: Methods for Taxonomic Classification of Prokaryotes

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

Author
Kristian Hovde Liland, Hilde Vinje, Lars Snipen
Date of publication
2016-09-08 10:46:46
Maintainer
Lars Snipen <lars.snipen@nmbu.no>
License
GPL (>= 2)
Version
1.0.1

View on CRAN

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

Files in this package

microclass
microclass/inst
microclass/inst/extdata
microclass/inst/extdata/rprob.mat.1400.rda
microclass/inst/extdata/std.frame.rda
microclass/inst/extdata/norm.models.rda
microclass/inst/extdata/rprob.mat.500.rda
microclass/inst/extdata/contax.trim.rda
microclass/inst/extdata/rprob.mat.300.rda
microclass/inst/extdata/rprob.mat.150.rda
microclass/src
microclass/src/rdpTrainCpp.cpp
microclass/src/Makevars
microclass/src/pow4int.cpp
microclass/src/charToInt.cpp
microclass/src/multinomTrainCpp.cpp
microclass/src/pow4inthead.h
microclass/src/KmerCount.cpp
microclass/src/Makevars.win
microclass/src/rdpClassifyCpp.cpp
microclass/src/RcppExports.cpp
microclass/src/multinomClassify.cpp
microclass/NAMESPACE
microclass/data
microclass/data/small.16S.rda
microclass/R
microclass/R/taxMachine.R
microclass/R/multinom.R
microclass/R/RcppExports.R
microclass/R/blast.R
microclass/R/rdpClassifier.R
microclass/R/KmerCount.R
microclass/R/datasets.R
microclass/R/zzz.R
microclass/R/microclass-package.R
microclass/MD5
microclass/DESCRIPTION
microclass/man
microclass/man/rdpClassify.Rd
microclass/man/rdpTrain.Rd
microclass/man/multinomTrain.Rd
microclass/man/microclass-package.Rd
microclass/man/multinomClassify.Rd
microclass/man/KmerCount.Rd
microclass/man/blastClassify16S.Rd
microclass/man/small.16S.Rd
microclass/man/blastDbase16S.Rd
microclass/man/setParallel.Rd
microclass/man/taxMachine.Rd