README: This repository contains metagenomic sequencing data and analysis scripts used to investigate the microbial communities in a pediatric pneumonia study (PediCAP) for my Master's thesis.

Purpose: This data and script are provided for transparency and reproducibility of the research conducted in my thesis.

Data: The data folder contains the files generated through Illumina NextSeq for analysis of perirectal samples from the PediCAP study. Metadata is supplied and is absent of all identifiers, additionally the knitted output files are supplied. File formats and additional information about the data can be found within the folders.

Scripts: The .Rmd files are markdown documents containing the different R codes used to analyze the sequencing data. These scripts require R (version 2023.12.1, build 402) and relevant packages to run.

Contact: For any inquiries or questions regarding the scripts, or the research presented in the thesis, please feel free to contact me. For other inquiries, please contact the university.

Note: This repository is for informational purposes only. The data may be subject to ethical considerations or restrictions depending on the PediCAP study protocols. Please contact the University of Antwerp, Laboratory of Medical Microbiology for further inquiries regarding the PediCAP study itself or the data displayed here.