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")):

Installation

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


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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DifferentialMethylation, DifferentialPeakCalling, MethylSeq, PeakDetection, RNASeq, Sequencing, Software
Version	1.10.0
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

Suggests	knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	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
Old Source Packages for BioC 3.16	Source Archive