Last updated: 2025-04-08

Checks: 2 0

Knit directory: DTU-code/analysis/

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Repository version: 59e7c06

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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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 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 DTU paper, which presents optimized differential transcript usage (DTU) pipelines using the latest versions of 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 RTA-induced dispersion from transcript isoform counts and account for the sparsity in 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 transcript-level differential expression 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 GSE227750).