diffReps

diffReps identifies differential peaks in Chromatin Immunoprecipitation sequencing (ChIP-seq) datasets to enable genome-wide comparison of histone modification enrichment between experimental conditions.

Key Features:

• Differential Site Detection: Detects differential sites from ChIP-seq data and accommodates analyses with or without biological replicates.
• Annotation of Differential Sites: Provides annotation of identified differential sites to supply contextual information.
• Identification of Chromatin Modification Hotspots: Identifies chromatin modification "hotspots," i.e., regions exhibiting concentrated changes in histone modifications.
• Implementation: Implemented in PERL and distributed as a command-line script for platform-independent execution.

Scientific Applications:

• Genome-wide histone modification profiling: Enables genome-wide profiling of histone modification marks across samples and conditions.
• Comparison between conditions: Compares ChIP-seq enrichment between experimental conditions such as disease versus control.
• ENCODE cell-line comparison: Applied to compare H3K4me3 histone marks between two human cell lines from the ENCODE project.
• In vivo brain tissue analysis: Applied to analyze H3K9me3 differences in a mouse brain region comparing cocaine- versus saline-treated conditions.

Methodology:

Scans the genome using a sliding window approach, performs millions of statistical tests to identify significant hits, and accounts for biological variation within sample groups.