manta: Microbial Assemblage Normalized Transcript Analysis

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Tools for robust comparative metatranscriptomics.

Author
Ginger Armbrust, Adrian Marchetti
Date of publication
None
Maintainer
Chris Berthiaume <chrisbee@uw.edu>, Adrian Marchetti <amarchetti@unc.edu>
License
Artistic-2.0
Version
1.20.0
URLs

View on Bioconductor

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

Files in this package

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