Project Reports

Introduction

Every student will work on a Course Project addressing a specific data analysis task within one of four major topic areas: Expression Profiling, AI/ML & Functional Interpretation, Single-cell Genomics, or Multi-omics Integration. The projects are organized as group projects with 2-3 students per sub-topic, where each student is assigned their own paper to present and analyze. Students will also present a scientific paper closely related to their project 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 Course Projects will be presented by each student during the last week of the course (see Slideshow Template here). In addition, each student will write a detailed analysis report for their assigned course project. The final project reports will be written in Quarto (.qmd). A basic tutorial on Quarto is available here. Both the Quarto source script (.qmd) 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 project needs to be organized in well-documented R functions in each project’s *_Fct.R script. The custom functions defined in *_Fct.R need to be imported (sourced) and used in the main .qmd project report. Other scripts used by the project need to be called from *_Fct.R (e.g. via R’s system function)

and also uploaded to the project repository. 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 project and include in it the following three files. All three files are mandatory.

  1. .qmd Quarto source script for the project report
  2. Report rendered from the .qmd source file in HTML or PDF format
  3. *_Fct.R file containing all helper functions written for the project, sourced and used in the corresponding Quarto report.

Submission Deadline for reports: 6:00 PM, June 9th, 2026

Structure of final project report

  1. Abstract
  2. Introduction
  3. Methods
    • Description of methods and tools used for the project
  4. Results and Discussion
    • All analysis steps, code, and results of the project
  5. Conclusions
  6. Acknowledgments
  7. References
  8. Supplement (optional)
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