Overview of Course Projects

3 minute read



Introduction

During the tutorial sessions of this class all students will perform the basic data analysis of one NGS Workflows including RNA-Seq, ChIP-Seq or VAR-Seq that is closely associated with their chosen Challenge Project. In addition, every student will work on a Challenge Project addressing a specific data analysis task within one of the general NGS Workflows. The Challenge projects are group projects organized by topics and 2-3 students in each group. Students will also present a scientific paper closely related to their challenge topic (see here). To facilitate teamwork and communication with the instructor, each course project will be assigned a private GitHub repository.

The results of the Challenge Projects will be presented by each student group during the last week of the course (see Slideshow Template here). In addition, each student will write a detailed analysis report for the assigned course project. This report needs to include all analysis steps of the corresponding Workflow Project (e.g. full RNA-Seq analysis) as well as the code and results of the Challenge Project. The final project reports will be written in R Markdown. A basic tutorial on R Markdown is available here. Both the R Markdown script (.Rmd) along with the rendered HTML or PDF report will be submitted to each student’s private project GitHub repository. All helper code used for the challenge project needs to be organized in well documented R functions of each project’s *_Fct.R script. The custom functions defined in *_Fct.R need to be imported (sourced) and used in the main Rmd project report. Other scripts used by the challenge projects need to be called from the *_Fct.R (e.g. via R’s system function) and also uploaded to the project repos. The expected structure of the final project report is outlined below.

The reports should be submitted to each student’s private project GitHub repository. For the report each student should create in this repository a new directory named after their workflow project and include in it the following files:

  • .Rmd source script of for both Workflow and Challenge Project, or two .Rmd source scripts, one for each: Workflow and Challenge Project.
  • Report(s) rendered from .Rmd source file(s) in HTML or PDF format.
  • ._Fct.R file containing all helper functions written for challenge project that is used in correponding R Markdown report.
  • Submission Deadline for reports: 6:00 PM, June 10th, 2025

Structure of final project report

  1. Abstract
  2. Introduction
  3. Methods
    • Short description of methods used by NGS workflow
    • Detailed description of methods used for challenge project
  4. Results and Discussion
    • Includes all components of NGS workflow as well as challenge project
  5. Conclusions
  6. Acknowledgments
  7. References
  8. Supplement (optional)
Last modified 2025-05-27: some edits (bcd8415)