Defining the Portfolio Project and Its Evidence

State the biological question, comparison, organism, and RNA-seq assay addressed by the project.

Draw a data-flow diagram linking each pipeline stage to its inputs, outputs, and quality checks.

Create a sample-and-metadata inventory that distinguishes raw data, derived data, code, and results.

Identify the assumptions currently embedded in the pipeline’s filenames, directory layout, and metadata.

Define measurable acceptance criteria for a successful run and a trustworthy differential-expression result.

Organize the repository so code, configuration, documentation, tests, and generated outputs have distinct locations.