ChroKit: a Shiny-based framework for interactive analysis, visualization and integration of genomic data.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Next-generation sequencing (NGS) experiments like ChIP-Seq and DNAse-Seq generate large genomic datasets.
• Analyzing and visualizing these enriched genomic regions requires specialized tools.

Purpose of the Study:

• To develop an interactive, web-based framework for intuitive exploration and analysis of genomic enrichment data.
• To provide a user-friendly platform for multidimensional analysis and visualization of NGS data.

Main Methods:

• Developed ChroKit, an R-based interactive framework.
• Implemented functionalities for genomic region manipulation, annotation, and signal enrichment calculation.
• Integrated unsupervised classification algorithms and logical operations for data refinement.
• Enabled interactive plotting with 'on the fly' re-analysis capabilities.

Main Results:

• ChroKit facilitates intuitive exploration and multidimensional analysis of genomic enrichment data.
• The tool supports interactive visualization and 'on the fly' data re-analysis.
• Exportable working sessions enhance reproducibility and data sharing.
• Multiplatform deployment optimizes computational speed and multi-user access.

Conclusions:

• ChroKit is a fast, intuitive, and versatile tool for analyzing genomic data from various NGS experiments.
• Its user-friendly graphical interface makes it accessible to a wide range of users.
• ChroKit promotes efficient data exploration, analysis, and collaboration within the bioinformatics community.