Package: DOTSeq 1.1.0

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_1.1.0.tar.gz
DOTSeq_1.1.0.zip(r-4.7)DOTSeq_1.1.0.zip(r-4.6)DOTSeq_1.1.0.zip(r-4.5)
DOTSeq_1.1.0.tgz(r-4.6-x86_64)DOTSeq_1.1.0.tgz(r-4.6-arm64)DOTSeq_1.1.0.tgz(r-4.5-x86_64)DOTSeq_1.1.0.tgz(r-4.5-arm64)
DOTSeq_1.1.0.tar.gz(r-4.7-arm64)DOTSeq_1.1.0.tar.gz(r-4.7-x86_64)DOTSeq_1.1.0.tar.gz(r-4.6-arm64)DOTSeq_1.1.0.tar.gz(r-4.6-x86_64)
DOTSeq_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DOTSeq/json (API)

# Install 'DOTSeq' in R:

install.packages('DOTSeq', repos = c('https://bioc.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)

riboseq singlecell generegulation geneexpression differentialexpression genetics sequencing software rnaseq bayesian regression multiplecomparison cpp

4.90 score 1 stars 8 scripts 190 downloads 25 exports 147 dependencies

Last updated from:8d37873b5e. Checks:1 WARNING, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	400
linux-devel-arm64	OK	638
linux-devel-x86_64	OK	734
source / vignettes	OK	721
linux-release-arm64	OK	629
linux-release-x86_64	OK	784
macos-release-arm64	OK	657
macos-release-x86_64	OK	1221
macos-oldrel-arm64	OK	395
macos-oldrel-x86_64	OK	1004
windows-devel	OK	792
windows-release	OK	764
windows-oldrel	OK	816
wasm-release	OK	346

Exports:.PostHoc calculateUsage countReads countReadsSingleCell DOTSeq DOTSeqDataSetsFromFeatureCounts DOTSeqDataSetsFromSummarizeOverlaps fitDOU fitResults getContrasts getContrasts<-getDOU getDOU<-getDTE getDTE<-getExonicReads getORFs mapIDs modelType plotDOT posthoc PostHoc show simDOT testDOU

Dependencies:abind AnnotationDbi ashr askpass backports BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob boot broom BSgenome cachem cigarillo cli codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray Deriv DESeq2 doBy dplyr emmeans estimability etrunct farver fastmap filelock forecast formatR fracdiff futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glmmTMB glue gtable hms httr httr2 invgamma IRanges irlba isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle lme4 lmtest locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minqa mixsqp modelr mvtnorm nlme nloptr nnet numDeriv openssl pbapply pbkrtest pillar pkgconfig png prettyunits progress purrr R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sandwich scales Seqinfo snow SparseArray SQUAREM stringi stringr SummarizedExperiment sys tibble tidyr tidyselect timeDate TMB truncnorm txdbmaker UCSC.utils urca utf8 vctrs viridisLite withr XML xml2 XVector yaml zoo

DOTSeq: Detecting Differential ORF Usage in Ribosome Profiling Data

Rendered fromDOTSeq.Rmdusingknitr::rmarkdown

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

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

Package: DOTSeq 1.1.0

DOTSeq: Genome-wide Detection of Differential ORF Usage

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