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 |