510 Final Projects Fall 20

Key Dates

Initial Project Outline & timeline (10%): Monday October 26th, End of Day as Github

• Title
• Author
• Overview of project:
  • 2 to 5 sentences describing overview
  • 1 to 2 sentences describing objectives, including
  • References/Links to Vignettes
• Data:
  • Identification of data, and demonstration of availability
• Milestone 1
  • One to five sentences describing measurable point
• Milestone 2
  • One to five sentences describing measurable point
• Deliverable
  • R MarkDown/Notebook/Jupyter.

Milestone 1 (10%): Tuesday November 3rd

Milestone 2/RC1 (10%): Thursday November 12th

Final Project Due Date: Friday November 17th: 11:50PM

Grading

• Plan (10%)
• Milestone 1 (10%)
• Milestone 2 (10%)
• Organization/Readability (25%)
• Repeatability (25%)
• Final Product (20%)

Examples:

• Choose a cancer and analysis from TCGA;
  • e.g. Hispanic Breast Cancer, Smokers vs. non-smokers. and complete analysis of Limma: https://www.bioconductor.org/packages/devel/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html
• Python
  • **Deep learning in genomics (Python) https://www.nature.com/articles/s41588-018-0295-5 ;
    • splice-site prediction
• Python/Bash
  • Germline variant calling, and identification of pathogenic variants using dbNSFP. (latter requires usage of python).
  • Tumor/germline mutation calling
    • • Requires COLO-829 FASTQ Set
• BASH/HPC
  • Tumor/germline mutation calling
    • Requires COLO-829 FASTQ Set
  • **Neoantigen-prediction pipeline
    • Requires COLO-829 dataset

Final Exam will multiple choice only: Due November 24th: 11:59PM