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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

Install

install.packages('manta')

Monthly Downloads

148

Version

1.18.0

License

Artistic-2.0

Maintainer

Chris Berthiaume

Last Published

October 10th, 2023

Functions in manta (1.18.0)

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