Epigenomics Workflow on Galaxy and Jupyter

Epigenomics Workflow on Galaxy and Jupyter provides a reproducible environment for processing ChIP-Seq and RNA-Seq data to analyze epigenomic regulation in Brassica rapa.

Key Features:

• Reproducibility: Docker containers encapsulate software and dependencies to ensure consistent computational environments.
• Integration of Galaxy and Jupyter: Combines Galaxy workflows with Jupyter notebooks to link workflow execution and interactive analysis.
• ChIP-Seq and RNA-Seq processing: Supports analysis of ChIP-Seq and RNA-Seq data for epigenomic and transcriptomic investigations.
• Designed for Brassica rapa: Initially tailored to analyze epigenomic datasets from Brassica rapa.
• Support for bioinformatics tools: Incorporates a wide range of bioinformatics tools within the Galaxy environment.
• Jupyter notebooks in Python and R: Provides interactive coding and documentation capabilities in Python or R for custom analyses.
• Containerization: Docker images package Galaxy, Jupyter, and dependencies to standardize execution.

Scientific Applications:

• Epigenomic profiling in Brassica rapa: Processing ChIP-Seq data to characterize epigenetic modifications in Brassica rapa.
• Transcriptome-epigenome integration: Combining RNA-Seq and ChIP-Seq analyses to investigate gene regulation mechanisms.
• Development of custom analyses: Enabling integration of custom scripts with existing workflows for method development and testing.

Methodology:

Docker images encapsulate Galaxy and Jupyter; Galaxy workflows execute a range of bioinformatics tools for ChIP-Seq and RNA-Seq processing; Jupyter notebooks provide interactive analysis and integration of custom scripts with Galaxy workflows.