derfinder

derfinder performs annotation-agnostic differential expression analysis of RNA-seq data to identify differentially expressed regions (DERs) across the genome.

Key Features:

• Base-level differential expression: Assesses differential expression at each genomic base to detect DERs independent of predefined gene boundaries or transcript assembly.
• Region-level segmentation: Segments contiguous bases with similar differential expression signals into regions and assigns statistical significance to each region.
• Annotation-optional analysis: Enables discovery without reference annotations while permitting optional annotation of DERs using reference genomic feature databases.
• Applicability to ChIP-seq: Applies the same approach to identify differentially bounded ChIP-seq peaks.

Scientific Applications:

• RNA-seq differential expression discovery: Unbiased genome-wide identification of differentially expressed regions in RNA-seq experiments.
• Regulatory element and non-coding RNA discovery: Detection of novel regulatory elements and non-coding RNAs that lie outside known gene boundaries.
• Chromatin and TF binding analysis: Analysis of chromatin dynamics and transcription factor binding variation via differential ChIP-seq peak boundaries.

Methodology:

Performs a genome-wide base-level assessment of differential expression, segments contiguous bases into regions based on similar differential expression signals, and assigns statistical significance to each region; annotation of DERs using reference genomic feature databases is optional.