Differential Expression Pipeline for an RNA-Seq Drug Discovery Run
Overview
What this challenge is about.
Build a Snakemake pipeline for RNA-Seq drug discovery: run fastp, salmon, tximport, and DESeq2 differential testing with QC plots. Get a verifiable certificate.
The scenario
The biotech (USD 35M annual revenue, 4 active client programs) cannot lose a month of contract work — the analysis must hold up when the lead bioinformatician returns and reviews it.
The Brief
What you'll do, and what you'll demonstrate.
Run a reproducible bulk-RNA-seq differential expression pipeline on a 16-sample experiment and produce a publication-quality report a senior bioinformatician will accept.
Earning criteria — what you'll demonstrate
- Orchestrate a bulk-RNA-seq analysis with a workflow manager
- Apply DESeq2 correctly including QC and contrast specification
- Communicate analytic decisions in a reviewable log
- Produce a publication-grade report on a contract-research timeline
Program Fit
Where this fits in your program.
Sharpens the same skills your degree expects you to demonstrate.
Aligned coursework coming soon.
Skills
Skills you'll demonstrate.
Each one shows up on your verified credential.
- Bioinformatics
Apply bioinformatics to solve real industry problems and demonstrate production-level capability.
- Computational Genomics
Apply computational genomics to solve real industry problems and demonstrate production-level capability.
- Differential Expression
Apply differential expression to solve real industry problems and demonstrate production-level capability.
- Workflow Orchestration
Apply workflow orchestration to solve real industry problems and demonstrate production-level capability.
- Reproducibility
Apply reproducibility to solve real industry problems and demonstrate production-level capability.
- Exploratory Data Analysis
Apply exploratory data analysis to solve real industry problems and demonstrate production-level capability.
Careers
Career paths this challenge builds toward
Completing this challenge demonstrates skills that transfer directly to these roles: