manta: Microbial Assemblage Normalized Transcript Analysis
Version 1.22.0

Tools for robust comparative metatranscriptomics.

Browse man pages Browse package API and functions Browse package files

AuthorGinger Armbrust, Adrian Marchetti
Bioconductor views DataImport DifferentialExpression GeneExpression Genetics QualityControl RNASeq Sequencing Visualization
Date of publicationNone
MaintainerChris Berthiaume <chrisbee@uw.edu>, Adrian Marchetti <amarchetti@unc.edu>
LicenseArtistic-2.0
Version1.22.0
URL http://manta.ocean.washington.edu/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("manta")

Man pages

cmdArgsToVariables: Create R variables from command line parameters
collapseRepliCounts: Collapse multiple technical replicate count columns into two...
compbiasPlot: plot the compositional bias for the sub-taxinomic rank
compbiasTest: compositional bias test
generateWeights: Generate Weights
in2manta: Convert a count or alignment table into a MANTA object
makeSampleDF: Make a Sample Dataframe for use in Initializing a MANTA...
manta: Create a MANTA object
manta-class: Microbial Assemblage Normalized Transcript Analysis - class
meta2counts: Convert a manta object's meta slot data into counts
metataxa2subcounts: create a new (sub) count table out of a subcomponent of the...
nf2nr: convert the normalization factors to a normalization line
normfact2absTMM: Convert a count or alignment table into a MANTA object
nr: Print out all the normalization ratios for each subset in a...
outliers: find the most significant or highest fold change outlier...
plot.manta: Plot a MAnTA object
pplacer2manta: convert a pplacer taxinomic placement repository to a MANTA...
readSeastar: Read SEAStAR output format
seastar2counts: Convert seastar output to count data
summary.manta: Summarize a MANTA object

Functions

MTDheatplot Source code
abs.nf Source code
aggBinCounts Source code
aggDESigCumDist Source code
align2manta Man page Source code
as.DGEList Source code
as.manta Source code
blncd.dvrst.ct Source code
calcLibSizeNormFact Source code
calcMTDexpnt Source code
calcTMMvar Source code
checkCondPair Source code
checkMetaLev Source code
cmdArgsToVariables Man page Source code
collapseRepliCounts Man page Source code
compbias Source code
compbiasPlot Man page Source code
compbiasTest Man page Source code
counts2manta Man page Source code
generateWeights Man page Source code
geomean.cmn.lib.size Source code
getCondFactor Source code
getCondGroups Source code
in2manta Man page
makeSampleDF Man page Source code
manta Man page Source code
manta-class Man page
manta.ra Man page
meta2counts Man page Source code
meta2metasum Source code
metataxa2subcounts Man page Source code
mtd Source code
nf2nr Man page Source code
normalize Source code
normfact2absTMM Man page Source code
nr Man page Source code
outGenes Man page Source code
plot.manta Man page
pplacer2manta Man page Source code
rawR Source code
readSeastar Man page Source code
seastar2counts Man page Source code
setLibrarySizes Source code
summary.manta Man page Source code
tableMetaSums Man page Source code
tableMetas Man page Source code
wtd.var Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/Aggregate.R
R/Checks.R
R/CompBias.R
R/Counts.R
R/DGE.R
R/Manta.R
R/Normalize.R
R/Outliers.R
R/Plot.R
R/Pplacer.R
R/Samples.R
R/Seastar.R
R/Summary.R
R/Util.R
R/Weights.R
R/in2manta.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/manta.R
inst/doc/manta.Rnw
inst/doc/manta.pdf
inst/extdata
inst/extdata/PapaGO-BLAST.results-diatoms.Rdata
inst/extdata/PapaGO-BLAST.results-diatoms.tab
inst/extdata/PapaGO-BWA.annot-diatoms.tab
inst/extdata/PapaGO-BWA.counts-diatoms.tab
inst/extdata/Pgranii-ambient.seastar
inst/extdata/Pgranii-plusFe.seastar
inst/extdata/pplacer
inst/extdata/pplacer/KOG0035
inst/extdata/pplacer/KOG0035/taxtable.db
inst/extdata/pplacer/KOG0119
inst/extdata/pplacer/KOG0119/taxtable.db
inst/extdata/pplacer/KOG0521
inst/extdata/pplacer/KOG0521/taxtable.db
inst/script
inst/script/manta.R
man
man/cmdArgsToVariables.Rd
man/collapseRepliCounts.Rd
man/compbiasPlot.Rd
man/compbiasTest.Rd
man/generateWeights.Rd
man/in2manta.Rd
man/makeSampleDF.Rd
man/manta-class.Rd
man/manta.Rd
man/meta2counts.Rd
man/metataxa2subcounts.Rd
man/nf2nr.Rd
man/normfact2absTMM.Rd
man/nr.Rd
man/outliers.Rd
man/plot.manta.Rd
man/pplacer2manta.Rd
man/readSeastar.Rd
man/seastar2counts.Rd
man/summary.manta.Rd
vignettes
vignettes/manta.Rnw
manta documentation built on May 20, 2017, 9:24 p.m.