exomePeak2

DOI: 10.18129/B9.bioc.exomePeak2    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see exomePeak2.

Bias-aware Peak Calling and Quantification for MeRIP-Seq

Bioconductor version: 3.13

exomePeak2 provides bias-aware quantification and peak detection for Methylated RNA immunoprecipitation sequencing data (MeRIP-Seq). MeRIP-Seq is a commonly applied sequencing technology that can measure the location and abundance of RNA modification sites under given cell line conditions. However, quantification and peak calling in MeRIP-Seq are sensitive to PCR amplification biases, which generally present in next-generation sequencing (NGS) technologies. In addition, the count data generated by RNA-Seq exhibits significant biological variations between biological replicates. exomePeak2 collectively address the challenges by introducing a series of robust data science tools tailored for MeRIP-Seq. Using exomePeak2, users can perform peak calling, modification site quantification and differential analysis through a straightforward single-step function. Alternatively, multi-step functions can be used to generate diagnostic plots and perform customized analyses.

Author: Zhen Wei [aut, cre]

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Coverage, DifferentialExpression, ExomeSeq, MethylSeq, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version	1.4.2
In Bioconductor since	BioC 3.11 (R-4.0) (1.5 years)
License	GPL (>= 2)
Depends	SummarizedExperiment, cqn
Imports	Rsamtools, GenomicAlignments, GenomicRanges, GenomicFeatures, DESeq2, ggplot2, mclust, genefilter, Biostrings, BSgenome, BiocParallel, IRanges, S4Vectors, reshape2, rtracklayer, apeglm, methods, stats, utils, Biobase, GenomeInfoDb, BiocGenerics
LinkingTo
Suggests	knitr, rmarkdown, RMariaDB
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_1.4.2.tar.gz
Windows Binary	exomePeak2_1.4.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	exomePeak2_1.4.2.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