PhD project of Tobias Zimmermann

Analysis of NGS data comes along with the requirements for computational infrastructure that allows the execution of relevant analysis tools without expert programming knowledge. We want to provide an R package, Petra, for epigenome and transcriptome analysis within the Bioconductor platform.

Petra will be accessible to the community to enable researchers to perform standard ChIP-seq, ATAC-seq, and RNA-seq analysis. In addition to basic workflows for the execution of principal analysis steps like differential expression/binding analysis and visualizations for exploratory analysis, we would like to integrate more specific and complex functionality dedicated to questions resulting from the combined analysis. For this purpose, we have implemented a super-enhancer detection algorithm based on peak position data. By combining different peak annotation approaches, a new peak to gene association algorithm has been designed. Additionally, functionality for the visualization of genomic data like browser snapshots, motif analysis, or correlation heat maps has been implemented.

The integration of transcriptome and epigenome data analysis will help put forward and test new hypotheses more efficiently. The R package Petra allows maximum flexibility to add new features. It provides a combined analysis of epigenome and transcriptome data - differential bound transcription factors and differentially expressed genes will be identified.