Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

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Documentation for package ‘anota2seq’ version 1.26.0

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

Help Pages

anota2seq-plots	Visualization of anota2seq results
anota2seqAnalyze	Analysis of translational activity
Anota2seqDataSet	Anota2seqDataSet class
Anota2seqDataSet-class	Anota2seqDataSet class
anota2seqDataSetFromMatrix	Anota2seqDataSet constructors.
anota2seqDataSetFromSE	Anota2seqDataSet constructors.
anota2seqGetContrasts	Accessor for the 'contrasts' slot of an Anota2seqDataSet object.
anota2seqGetContrasts-method	Accessor for the 'contrasts' slot of an Anota2seqDataSet object.
anota2seqGetCovariates	Accessor for the 'phenoVec' and 'batchVec' slots of an Anota2seqDataSet object.
anota2seqGetCovariates-method	Accessor for the 'phenoVec' and 'batchVec' slots of an Anota2seqDataSet object.
anota2seqGetDeltaData	Accessor for the fold changes and TE scores stored in the 'deltaData' slot of an Anota2seqDataSet object.
anota2seqGetDeltaData-method	Accessor for the fold changes and TE scores stored in the 'deltaData' slot of an Anota2seqDataSet object.
anota2seqGetNormalizedData	Accessor for the 'normalizedDataP' and 'normalizedDataT' slots of an Anota2seqDataSet object.
anota2seqGetNormalizedData-method	Accessor for the 'normalizedDataP' and 'normalizedDataT' slots of an Anota2seqDataSet object.
anota2seqGetOutput	Retrieve output for analyzes stored in the Anota2seqDataSet
anota2seqGetOutput-method	Retrieve output for analyzes stored in the Anota2seqDataSet
anota2seqGetQualityControl	Retrieve the anota2seqPerformQC output from the Anota2seqDataSet
anota2seqGetQualityControl-method	Retrieve the anota2seqPerformQC output from the Anota2seqDataSet
anota2seqGetResidOutlierTest	Retrieve residOutlierTest
anota2seqGetResidOutlierTest-method	Retrieve residOutlierTest
anota2seqGetThresholds	Get filtering criteria thresholds
anota2seqGetThresholds-method	Get filtering criteria thresholds
anota2seqPerformQC	Perform quality control to ensure that the supplied data set is suitable for Analysis of Partial Variance (APV) within anota2seq.
anota2seqPlotFC	Visualization of anota2seq results
anota2seqPlotFC-method	Visualization of anota2seq results
anota2seqPlotGenes	Visualization of anota2seq results
anota2seqPlotGenes-method	Visualization of anota2seq results
anota2seqPlotPvalues	Visualization of anota2seq results
anota2seqPlotPvalues-method	Visualization of anota2seq results
anota2seqRegModes	Categorize genes into regulatory modes of gene expression (mRNA abundance or changes in translational efficiency leading to altered protein levels or buffering)
anota2seqResidOutlierTest	Test for normality of residuals
anota2seqRun	Wrapper for several functions which provide one-step analysis
anota2seqSelSigGenes	Select identifiers from the output of 'anota2seqAnalyze'.
anota2seq_data	Sample data set for anota2seq
anota2seq_data_P	Sample data set for anota2seq
anota2seq_data_T	Sample data set for anota2seq
anota2seq_pheno_vec	Sample data set for anota2seq
show	Show information for an Anota2seqDataSet
show-method	Show information for an Anota2seqDataSet