DOTSeq

Genome-wide Detection of Differential ORF Usage

Bioconductor version: 3.23 · Package version: 1.0.0

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DOTSeq")