exomePeak2

DOI: 10.18129/B9.bioc.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 (3.16)

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")

# 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")

 

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

Details

biocViews Coverage, DifferentialMethylation, DifferentialPeakCalling, MethylSeq, PeakDetection, RNASeq, Sequencing, Software
Version 1.9.1
In Bioconductor since BioC 3.11 (R-4.0) (2.5 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
LinkingTo
Suggests knitr, rmarkdown
SystemRequirements
Enhances
URL
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_1.9.1.tar.gz
Windows Binary exomePeak2_1.9.1.zip (64-bit only)
macOS 10.13 (High Sierra) exomePeak2_1.9.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/exomePeak2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/exomePeak2
Package Short Url https://bioconductor.org/packages/exomePeak2/
Package Downloads Report Download Stats

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