# Microbial Assemblage Normalized Transcript Analysis

## Documentation for package ‘manta’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

align2manta | Convert a count or alignment table into a MANTA object
cmdArgsToVariables | Create R variables from command line parameters
collapseRepliCounts | Collapse multiple technical replicate count columns into two columns for plotting
compbiasPlot | plot the compositional bias for the sub-taxinomic rank
compbiasTest | compositional bias test
counts2manta | Convert a count or alignment table into a MANTA object
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 object
manta | Create a MANTA object
manta-class | Microbial Assemblage Normalized Transcript Analysis - class
manta.ra | Plot a MAnTA object
meta2counts | Convert a manta object's meta slot data into counts
metataxa2subcounts | create a new (sub) count table out of a subcomponent of the metatranscriptome
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 specified taxinomic rank of a manta object
outGenes | find the most significant or highest fold change outlier genes
plot.manta | Plot a MAnTA object
pplacer2manta | convert a pplacer taxinomic placement repository to a MANTA object
readSeastar | Read SEAStAR output format
seastar2counts | Convert seastar output to count data
summary.manta | Summarize a MANTA object
tableMetas | Convert a count or alignment table into a MANTA object
tableMetaSums | Convert a count or alignment table into a MANTA object