exomePeak2

DOI: 10.18129/B9.bioc.exomePeak2    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see exomePeak2.

Bias Awared Peak Calling and Quantification for MeRIP-Seq

Bioconductor version: 3.12

exomePeak2 provides bias awared quantification and peak detection on Methylated RNA immunoprecipitation sequencing data (MeRIP-Seq). MeRIP-Seq is a commonly applied sequencing technology to measure the transcriptome-wide location and abundance of RNA modification sites under a given cellular condition. However, the quantification and peak calling in MeRIP-Seq are sensitive to PCR amplification bias which is prevalent in next generation sequencing (NGS) techniques. In addition, the RNA-Seq based count data exhibits biological variation in small reads count. exomePeak2 collectively address these challanges by introducing a rich set of robust data science models tailored for MeRIP-Seq. With exomePeak2, users can perform peak calling, modification site quantification, and differential analysis with a straightforward one-step function. Alternatively, users could define personalized methods for their own analysis through multi-step functions and diagnostic plots.

Author: Zhen Wei

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

Installation

To install this package, start R (version "4.0") 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, ImmunoOncology, MethylSeq, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.11 (R-4.0) (1 year)
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
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_1.2.0.tar.gz
Windows Binary	exomePeak2_1.2.0.zip
macOS 10.13 (High Sierra)	exomePeak2_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/exomePeak2
Source Repository (Developer Access)	git clone [email protected]:packages/exomePeak2
Package Short Url	https://bioconductor.org/packages/exomePeak2/
Package Downloads Report	Download Stats