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. Each student is assigned an individual sub-project with its own paper, analysis tasks, and report (for details see Course Planning sheet). Students working within the same topic area form a group to facilitate cross-comparisons and shared data analysis where applicable, but each student presents and reports on their own sub-project independently. Students will also present a scientific paper closely related to their assigned sub-project (see here). Each student will be assigned their own private GitHub repository for their project; students within the same topic area can be granted read access to each other’s repositories to facilitate collaboration and cross-comparisons.

The results of the assigned sub-projects will be presented by each student separately during the last week of the course (see Slideshow Template here). Since the topics within each group are related, the presentations within a group will be held in sequence where group members want to minimize duplication, e.g. shared data sets and results need to be presented only once. 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 developed for the assigned project tasks need 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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