BVCN Reproducibility Challenge
Welcome to the Reproducibility Tutorial and Challenge!
Guided Reproducibility Tutorial
1. The Point of this Tutorial
1.1 What is reproducibility, anyway?
1.2 Why are we interested in reproducibility?
1.3 Links to other example reproducibility projects
2. Getting Started
2.1 How does one identify a good bioinformatics paper to reproduce?
2.2 How does one organize a bioinformatics project?
3. Transcriptomics & Zebrafish
3.1 Sample Study Background
3.1.1 What kind of a bioinformatics project is this?
3.1.2 What do they mean by that?
3.2 Breaking Down the Process
3.2.1 Stumbling blocks getting started
3.2.2 How we fleshed it out in `bash`
3.3 How Did We Do?
3.3.1 Pipelining and differential expression analysis (Python)
3.3.2 Data analysis and visualization (Python)
4. Population Genomics & Lobsters
4.1 Sample Study Background
4.1.1 Interpreting their analysis
4.1.2 Breaking down the jargon
4.2 Breaking Down the Process
4.2.1 Population Differentiation (Original R)
5. Provide feedback to the team!
Reproducibility Challenge
6. Reproducibility Challenge
6.1 Introduction to this project
6.2 What's the point of all this?
6.3 Getting started on your project
7. Instructions and Timeline
7.1 Writing a proposal
7.2 Finding a mentor
7.3 Timeline for the Challenge
7.4 Products of the challenge
8. Sign Up Here
8.1 Instructors, click here!
8.2 Students, click here!
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Jupyter Book
.ipynb
.pdf
Interact with Binder
Links to other example reproducibility projects
Coral metatranscriptome analysis paper
(Daniels et al., 2015)
GitHub
repository for reproduction
Genome streamlining in plankton
(Swan et al., 2013)
GitHub
repository for reproduction
