Bachelor-Thesis

Code repository containing the scripts used for the analysis in my Bachelor Thesis Machine Learning Based Gene Expression Prediction from ChIP-seq Signal in Lactation.

The code in this repository can be divided into three sections:

• Preprocessing of the datasets (ChIP-seq and RNA-seq) using nf-core[1]
• Analysis of the data using DESeq2[2], TEPIC[3] and DYNAMITE[4]
• Visualization and verification of the results

Preprocessing of the datasets

01_Preprocessing contains scripts used to:

• Download all the raw fastq files from GEO IDs
• Count the number of biological replicates
• Check for duplicate files
• Create the the input.csv needed for the nf-core/chip-seq pipeline

Analysis of the data

02_Analysis contains scripts used to:

• Generate and visualize the output for DESeq2
• Generate the output for TEPIC
• Setup the configuration files for DYNAMITE

Visualization and verification of the results

03_Visualization_and_Verification contains scripts to:

• Verify the results of TEPIC (creating PR-AUC scores)
• Visualize the results of DYNAMITE.