Rifampicin_omics_integration

Description

This repository for the multi-omics data analysis including MeDIP-seq, RNA-seq, and proteomics, for Chapter 4 of my PhD thesis.

Instructions

• The data folder stores all the needed data information
• The outcome folder stores all the results of the data analysis
• The prepare_samples folder contains bash script to processing raw data (.fastq files) before running the analysis code in R
• The RNAseq_RODAF is the script to run the RNAseq data using the R-ODAF
• The R_codes is the R scripts to analyse the proteomics data (for previous work)
• The Rif_data_analysis is the R script each omics data (MeDIP-seq, RNA-seq, and proteomics) - single omics anlysis
• The TF_target_analysis is the R script to do the transcription factor (TF) - target analysis among the outcome of single omics analysis
• The output, reference, and sample folders are for running the RegOmics tool to identify TF-target relations

Related publications

For the DNA methylation anlysis, I used the same workflow as the previous publication: Nguyen, Nhan et al. “A bioinformatics workflow to detect genes with DNA methylation alterations: a case study of analyzing MeDIP-seq data in cardiac microtissue exposed to epirubicin”. International Conference Proceedings by ACM (2022). https://doi.org/10.1145/3510427.3510437

Contact:

LinkedIn: nhannguyen | ORCID: 0000-0001-8720-1195