exomePeak

exomePeak detects and analyzes N6-methyladenosine (m(6)A) modifications from MeRIP-seq (methylated RNA immunoprecipitation sequencing) data to identify sites and perform differential analysis of RNA methylation.

Key Features:

• RNA Methylation Site Detection: Identifies specific N6-methyladenosine (m(6)A) sites from MeRIP-seq data under defined experimental conditions.
• Differential Analysis: Provides functions to compare two experimental conditions and detect differential m(6)A methylation across transcripts.
• Comprehensive Protocol: Implements a protocol covering steps from raw read alignment to downstream functional analysis for MeRIP-seq data.
• Motif Discovery and Functional Analysis: Supports motif discovery and functional analysis to investigate biological implications of RNA modifications.

Scientific Applications:

• RNA Epigenetics Research: Enables studies of how m(6)A modifications influence gene expression and cellular processes.
• Transcriptome-wide Mapping: Facilitates transcriptome-wide mapping of post-transcriptional RNA modifications using MeRIP-seq data.
• Differential Methylation Studies: Supports case-control and comparative studies of development, disease progression, and responses to environmental stimuli via differential methylation analysis.

Methodology:

Computational steps explicitly include alignment of raw reads, detection of methylation sites, motif discovery, and differential methylation analysis; the software is implemented as an R/Bioconductor package and builds on a MATLAB package framework (Meng, Jia, et al., 2013).