ChIP-Seq Analysis Script

Overview

This repository contains an R script for analyzing ChIP-Seq data, specifically for histone modifications such as H3K27Ac, H3K27me3, and H3K4me1. The script uses popular bioinformatics libraries like ChIPseeker, clusterProfiler, and ReactomePA to perform data visualization, functional enrichment analysis, and peak annotation.

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Features

1. Peak Analysis

• Visualizes ChIP-Seq peaks across chromosomes.
• Generates heatmaps and average profile plots.

2. Peak Annotation

• Annotates peaks relative to genomic regions such as TSS (transcription start sites).
• Produces pie charts, bar plots, and upset plots for genomic annotation.

3. Functional Enrichment

• Enriches pathways using the Reactome database.
• Visualizes pathway analysis results with dot plots and enrichment maps.

4. Data Comparison

• Compares ChIP-Seq datasets.
• Profiles multiple datasets with heatmaps, bar plots, and TSS binding visualizations.

5. Statistical Testing

• Conducts statistical testing for ChIP-Seq overlap enrichment.

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Dependencies

The following R packages are required to run the script:

• RColorBrewer
• ChIPseeker
• clusterProfiler
• TxDb.Mmusculus.UCSC.mm10.knownGene
• ReactomePA

To install these packages, run:

install.packages("RColorBrewer")
BiocManager::install(c("ChIPseeker", "clusterProfiler", "TxDb.Mmusculus.UCSC.mm10.knownGene", "ReactomePA"))