Last updated: 2025-08-27

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Knit directory: DTU-code/analysis/

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 5951235 Pedro Baldoni 2025-08-27 DTU paper revision
html cb83e05 Pedro Baldoni 2025-04-08 Build site.
Rmd 9bbfdca Pedro Baldoni 2025-04-08 Update landing page
Rmd cd0ad9d Pedro Baldoni 2024-05-01 Start workflowr project.

This website hosts code for the paper presenting optimized differential transcript usage (DTU) pipelines using the the R/Bioconductor packages edgeR and limma.

The presented pipeline builds upon the latest developments of edgeR and limma with a unified interface via the diffSplice function. The pipelines make use of divided counts to remove the RTA-induced dispersion and account for the sparsity from transcript-level counts. The new diffSplice pipelines provide greater power, improved efficiency, and improved FDR control compared to existing specialized DTU methods.

Simulation study

The pages below present the necessary steps to rerun our simulation study and the code used to generate the figures and tables from the main and supplementary texts of the DTU paper.

Case study

The pages below present the data pre-processing steps and analysis report of the RNA-seq experiments from the steady-state adult mouse mammary gland (GEO accession GSE227748).