Package: DOTSeq 1.0.0

Chun Shen Lim

DOTSeq: Genome-wide Detection of Differential ORF Usage

Differential open reading frame (ORF) translation analysis framework for ribosome profiling (Ribo-seq) with matched RNA-seq. Implements (i) Differential ORF Usage (DOU), a beta-binomial generalized linear model that models the expected proportion of Ribo-seq versus RNA-seq reads mapping to each ORF within a gene, and (ii) ORF-level Differential Translation Efficiency (DTE), a negative binomial GLM that capture changes in translation efficiency of individual ORFs across experimental conditions. Supports ORF-level read summarization for bulk and single-cell Ribo-seq.

Authors:Chun Shen Lim [aut, cre], Gabrielle Chieng [aut, ctb], Marsden [fnd]

DOTSeq_1.0.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
DOTSeq/json (API)
NEWS

# Install 'DOTSeq' in R:
install.packages('DOTSeq', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/compgenom/dotseq/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:DOTSeq-1.1.0(bioc 3.24)DOTSeq-1.0.0(bioc 3.23)

riboseqsinglecellgeneregulationgeneexpressiondifferentialexpressiongeneticssequencingsoftwarernaseqbayesianregressionmultiplecomparisoncpp

4.90 score 1 stars 190 downloads 25 exports 148 dependencies

Last updated from:7717b3ef59 (on RELEASE_3_23). Checks:1 NOTE, 13 OK. Indexed: no.

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source / vignettesOK708
linux-release-arm64OK674
linux-release-x86_64OK783
macos-release-arm64OK648
macos-release-x86_64OK1115
macos-oldrel-arm64OK483
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wasm-releaseOK345

Exports:.PostHoccalculateUsagecountReadscountReadsSingleCellDOTSeqDOTSeqDataSetsFromFeatureCountsDOTSeqDataSetsFromSummarizeOverlapsfitDOUfitResultsgetContrastsgetContrasts<-getDOUgetDOU<-getDTEgetDTE<-getExonicReadsgetORFsmapIDsmodelTypeplotDOTposthocPostHocshowsimDOTtestDOU

Dependencies:abindAnnotationDbiashraskpassbackportsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootbroomBSgenomecachemcigarilloclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivDESeq2doBydplyremmeansestimabilityetrunctfarverfastmapfilelockforecastformatRfracdifffutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glmmTMBgluegtablehmshttrhttr2invgammaIRangesirlbaisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamixsqpmodelrmvtnormnlmenloptrnnetnumDerivopensslpbapplypbkrtestpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sandwichscalesSeqinfosnowSparseArraySQUAREMstringistringrSummarizedExperimentsystibbletidyrtidyselecttimeDateTMBtruncnormtxdbmakerUCSC.utilsurcautf8vctrsviridisLitewithrXMLxml2XVectoryamlzoo

DOTSeq: Detecting Differential ORF Usage in Ribosome Profiling Data

Chun Shen Lim, Gabrielle S.W. Chieng

Rendered fromDOTSeq.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-03-17
Started: 2025-08-17

Readme and manuals

Help Manual

Help pageTopics
Calculate ORF usage across conditions from a SummarizedExperimentcalculateUsage
Count reads from BAM files over genomic featurescountReads
Count single-cell reads/UMIs from BAM over genomic features (optimized)countReadsSingleCell
DOTSeq: Differential Analysis of Translation Efficiency and Usage of Open Reading FramesDOTSeq-package DOTSeq
DOTSeqDataSets-classDOTSeqDataSets-class show,DOTSeqDataSets-method
Construct DOTSeqDatasets from featureCounts output for Differential ORF Translation AnalysisDOTSeqDataSetsFromFeatureCounts DOTSeqDataSetsFromSummarizeOverlaps
DOUData-classDOUData-class
Validity method for DOUDataDOUData-validity
DTEData-classDTEData-class
Find ORFs in FASTA sequences using ORFik's C++ enginefindORFsFasta
Fit Differential ORF Usage ModelsfitDOU
Access and replace contrast results from post hoc analysisgetContrasts getContrasts,DOTSeqDataSets-method getContrasts,DOUData-method getContrasts,DTEData-method getContrasts<- getContrasts<-,DOUData-method getContrasts<-,DTEData-method
Accessor and replacement methods for DOU slotgetDOU getDOU,DOTSeqDataSets-method getDOU<- getDOU<-,DOTSeqDataSets-method
Accessor and replacement methods for DTE slotgetDTE getDTE,DOTSeqDataSets-method getDTE<- getDTE<-,DOTSeqDataSets-method
Filter BAM files to retain only reads overlapping exonic regionsgetExonicReads
Extract Genomic ORFs from Transcript SequencesgetORFs
Retrieve Gene Symbols from Ensembl or Ensembl GenomesmapIDs
Access the model type from a PostHoc objectfitResults fitResults,PostHoc-method modelType modelType,PostHoc-method posthoc posthoc,PostHoc-method
Get list of the number of exons per groupnumExonsPerGroup
Generate Differential ORF Translation (DOT) Visualization SuiteplotDOT
Construct a PostHoc ObjectPostHoc
The PostHoc class for DOTSeq.PostHoc PostHoc-class
Remove random effects from a formularemove_random_effects
Simulate Differential ORF Translation (DOT)simDOT
Compute Differential ORF Usage (DOU) Contrasts Using EMMstestDOU