| 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 |