exomePeak2

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see exomePeak2.

Bias Awared Peak Calling and Quantification for MeRIP-Seq


Bioconductor version: 3.11

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>

Citation (from within R, enter citation("exomePeak2")):

Installation

To install this package, start R (version "4.0") 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

Details

biocViews Coverage, DifferentialExpression, ExomeSeq, ImmunoOncology, MethylSeq, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL (>= 2)
Depends SummarizedExperiment, cqn
Imports Rsamtools, GenomicAlignments, GenomicRanges, GenomicFeatures, DESeq2, ggplot2, mclust, genefilter, Biostrings, BSgenome, BiocParallel, IRanges, S4Vectors, reshape2, rtracklayer, apeglm, RMariaDB, methods, stats, utils, Biobase, GenomeInfoDb
System Requirements
URL
Bug Reports https://github.com/ZW-xjtlu/exomePeak2/issues
See More
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_1.0.0.tar.gz
Windows Binary exomePeak2_1.0.0.zip
macOS 10.13 (High Sierra) exomePeak2_1.0.0.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 3.11 Source Archive