Microbial Assemblage Normalized Transcript Analysis


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Documentation for package ‘manta’ version 1.24.0

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