Interactive ChIP-Seq peak analysis with Shiny: overlap detection, peak annotation, width comparison, and visualization.
✨ Features
- Peak overlap analysis with custom Venn diagrams
- Peak annotation using ChIPseeker + TxDb.Hsapiens.UCSC.hg38
- Width comparison density plots
- Export tables (Excel) and plots (PDF)
- Multi-sample filtering by p-value and overlap count
🚀 Installation
Install: devtools::install_github(“YOURUSERNAME/bccAnalysis”)
Load package: library(bccAnalysis)
🎛️ Shiny App Interface
| Tab | Features |
|---|---|
| Load Files | Upload .rds GRangesList, select samples, set overlap filters |
| Venn Diagram | Visual peak overlap between conditions |
| Table of Overlaps | Downloadable proportions + peak counts |
| Width Comparison | Log-scale density plot |
| Peak Analysis | Annotation barplots (main/unique/overlap peaks) |
🔗 Dependencies
- Bioconductor:
GenomicRanges,rtracklayer,TxDb.Hsapiens.UCSC.hg38.knownGene,ChIPseeker - CRAN:
shiny,bslib,ggplot2,writexl,tibble,gridExtra
🙏 Acknowledgments
Built with using R package development best practices from Hadley Wickham.