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manta (version 1.18.0)
Microbial Assemblage Normalized Transcript Analysis
Description
Tools for robust comparative metatranscriptomics.
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Version
Version
1.18.0
1.16.0
1.14.0
1.12.0
1.0.1
1.0.0
Install
install.packages('manta')
Monthly Downloads
151
Version
1.18.0
License
Artistic-2.0
Maintainer
Chris Berthiaume
Last Published
October 10th, 2023
Functions in manta (1.18.0)
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metataxa2subcounts
create a new (sub) count table out of a subcomponent of the metatranscriptome
makeSampleDF
Make a Sample Dataframe for use in Initializing a MANTA object
compbiasPlot
plot the compositional bias for the sub-taxinomic rank
summary.manta
Summarize a MANTA object
generateWeights
Generate Weights
manta
Create a MANTA object
plot.manta
Plot a MAnTA object
collapseRepliCounts
Collapse multiple technical replicate count columns into two columns for plotting
meta2counts
Convert a manta object's meta slot data into counts
in2manta
Convert a count or alignment table into a MANTA object
nf2nr
convert the normalization factors to a normalization line
seastar2counts
Convert seastar output to count data
readSeastar
Read SEAStAR output format
normfact2absTMM
Convert a count or alignment table into a MANTA object
cmdArgsToVariables
Create R variables from command line parameters
manta-class
Microbial Assemblage Normalized Transcript Analysis - class
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
compbiasTest
compositional bias test
pplacer2manta
convert a pplacer taxinomic placement repository to a MANTA object