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exomePeak2

This is the development version of exomePeak2; for the stable release version, see exomePeak2.

Peak Calling and differential analysis for MeRIP-Seq


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("exomePeak2")

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

Documentation

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

browseVignettes("exomePeak2")
The exomePeak2 user's guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DifferentialMethylation, DifferentialPeakCalling, MethylSeq, PeakDetection, RNASeq, Sequencing, Software
Version 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements
URL
Bug Reports https://github.com/ZW-xjtlu/exomePeak2/issues
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package exomePeak2_1.15.0.tar.gz
Windows Binary exomePeak2_1.15.0.zip
macOS Binary (x86_64) exomePeak2_1.15.0.tgz
macOS Binary (arm64) exomePeak2_1.15.0.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