DOI: 10.18129/B9.bioc.exomePeak2  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see exomePeak2.

Peak Calling and differential analysis for MeRIP-Seq

Bioconductor version: 3.16

exomePeak2 provides peak detection and differential methylation for Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) data. MeRIP-Seq is a commonly applied sequencing assay that measures the location and abundance of RNA modification sites under specific cellular conditions. In practice, the technique is sensitive to PCR amplification biases commonly found in NGS data. In addition, the efficiency of immunoprecipitation often varies between different IP samples. exomePeak2 can perform peak calling and differential analysis independent of GC content bias and IP efficiency changes.

Author: Zhen Wei [aut, cre]

Maintainer: Zhen Wei <zhen.wei10 at icloud.com>

Citation (from within R, enter citation("exomePeak2")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script The exomePeak2 user's guide
PDF   Reference Manual
Text   NEWS


biocViews Coverage, DifferentialMethylation, DifferentialPeakCalling, MethylSeq, PeakDetection, RNASeq, Sequencing, Software
Version 1.10.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License Artistic-2.0
Depends R (>= 3.5.0), SummarizedExperiment
Imports Rsamtools, GenomicAlignments, GenomicRanges, GenomicFeatures, DESeq2, ggplot2, mclust, BSgenome, Biostrings, GenomeInfoDb, BiocParallel, IRanges, S4Vectors, rtracklayer, methods, stats, utils, BiocGenerics, magrittr, speedglm, splines
Suggests knitr, rmarkdown
BugReports https://github.com/ZW-xjtlu/exomePeak2/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package exomePeak2_1.10.0.tar.gz
Windows Binary exomePeak2_1.10.0.zip (64-bit only)
macOS Binary (x86_64) exomePeak2_1.10.0.tgz
macOS Binary (arm64) exomePeak2_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/exomePeak2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/exomePeak2
Bioc Package Browser https://code.bioconductor.org/browse/exomePeak2/
Package Short Url https://bioconductor.org/packages/exomePeak2/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: