trackViewer

trackViewer visualizes mapped reads and annotation layers from next-generation sequencing (NGS) datasets to support interpretation of genomic features.

Key Features:

• Multi-Track Visualization: Enables simultaneous visualization and overlay of multiple track layers representing mapped reads and annotations.
• Supported NGS Data Types: Supports visualization of ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs, and methylation data.
• Integration with Bioconductor: Integrates with the Bioconductor ecosystem to use R-based genomic analysis packages and data structures.
• Interoperability: Interoperates with other Bioconductor packages to incorporate analytical workflows and exchange genomic data objects.
• Formal Review and Testing: Benefits from Bioconductor's formal initial review and continuous automated testing processes.

Scientific Applications:

• ChIP-seq Analysis: Visualizes protein–DNA interactions and binding sites from ChIP-seq mapped reads.
• RNA-seq Studies: Displays RNA-seq read coverage and annotations to examine gene expression profiles and support identification of differentially expressed genes.
• miRNA-seq Investigations: Visualizes miRNA-seq expression patterns and annotations to study miRNA regulatory roles.
• DNA-seq and SNP Analysis: Shows DNA-seq coverage and SNP locations to support analysis of genetic variation and GWAS-related visualization.
• Methylation Data Exploration: Visualizes DNA methylation patterns alongside annotations for epigenetic analysis.

Methodology:

Visualization and track overlay are implemented in R using Bioconductor data structures and R's statistical programming capabilities.