Project Contributors

Group09:
Selina Friesen - s252027 - SeFrie
Marta Sanchez Sanchez - s254791 - martasanchez99
Sergi Fornos - s253693 - SergiFornos
Tommaso Ballocci - s257151 - tobal-r
Ivan Musalyk - - Ivan Mus

Project Overview

This repository implements the required R4BDS project structure.

The project analyses epitope-level CD8 T cell responses against SARS-CoV-2, based on the dataset from Saini et al., Sci Immunol 2021.

Data Retrieval

Raw data are NOT stored on GitHub.

Place the raw data file(s) in:

• data/_raw/raw_data.xlsx

or adapt the file name and path in R/01_load.qmd. If programmatic retrieval is possible, implement it in 01_load.qmd and describe access in a safe way.

Project Structure

• data/_raw/ – raw, untouched data

• data/01_dat_load.tsv – loaded / combined data

• data/02_dat_clean.tsv – cleaned, tidy data

• data/03_dat_aug.tsv – data with derived variables

• R/01_load.qmd – load raw data

• R/02_clean.qmd – clean and tidy data

• R/03_augment.qmd – add derived variables

• R/04_describe.qmd – descriptive statistics

• R/05_analysis_1.qmd – first main analysis

• R/06_analysis_2.qmd – second main analysis

• R/99_proj_func.qmd – helper functions

• R/00_all.qmd – master document to orchestrate the full pipeline

• results/ – HTML outputs and key plots

• doc/presentation.qmd – final Quarto presentation

• doc/presentation.html – rendered self-contained presentation

Presentation Link

Add the direct link generated with raw.githack, for example:

https://raw.githack.com////doc/presentation.html