# Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

## Documentation for package ‘anota2seq’ version 1.6.0

- 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