DOTSeq                  DOTSeq: Differential Analysis of Translation
                        Efficiency and Usage of Open Reading Frames
DOTSeqDataSets-class    DOTSeqDataSets-class
DOTSeqDataSetsFromFeatureCounts
                        Construct DOTSeqDatasets from featureCounts
                        output for Differential ORF Translation
                        Analysis
DOUData-class           DOUData-class
DOUData-validity        Validity method for DOUData
DTEData-class           DTEData-class
PostHoc                 Construct a PostHoc Object
PostHoc-class           The PostHoc class for DOTSeq
calculateUsage          Calculate ORF usage across conditions from a
                        SummarizedExperiment
countReads              Count reads from BAM files over genomic
                        features
findORFsFasta           Find ORFs in FASTA sequences using ORFik's C++
                        engine
fitDOU                  Fit Differential ORF Usage Models
getContrasts            Access and replace contrast results from post
                        hoc analysis
getDOU                  Accessor and replacement methods for DOU slot
getDTE                  Accessor and replacement methods for DTE slot
getExonicReads          Filter BAM files to retain only reads
                        overlapping exonic regions
getORFs                 Extract Genomic ORFs from Transcript Sequences
mapIDs                  Retrieve Gene Symbols from Ensembl or Ensembl
                        Genomes
modelType               Access the model type from a PostHoc object
numExonsPerGroup        Get list of the number of exons per group
plotDOT                 Generate Differential ORF Translation (DOT)
                        Visualization Suite
remove_random_effects   Remove random effects from a formula
simDOT                  Simulate Differential ORF Translation (DOT)
testDOU                 Compute Differential ORF Usage (DOU) Contrasts
                        Using EMMs
