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This package performs a Gene Set Analysis with the approach adopted by PADOG on the genes that are reported as translationally regulated (ie. exhibit a significant change in TE) by the DeltaTE package. It can be used on its own to see the impact of translation regulation on gene sets, but it is also integrated as an additional analysis method within ReactomeGSA, where results are further contextualised in terms of pathways and directionality of the change.
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.