exomePeak

DOI: 10.18129/B9.bioc.exomePeak    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see exomePeak.

exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis

Bioconductor version: 3.9

The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng if you have any questions.

Author: Lin Zhang <lin.zhang at cumt.edu.cn>, Lian Liu <liulian19860905 at 163.com>, Jia Meng <jia.meng at xjtlu.edu.cn>

Maintainer: Lin Zhang <lin.zhang at cumt.edu.cn>, Lian Liu <liulian19860905 at 163.com>, Jia Meng <jia.meng at xjtlu.edu.cn>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("exomePeak")

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("exomePeak")

 

PDF	R Script	An introduction to exomePeak
PDF		Reference Manual
Text		NEWS

Details

biocViews	HighThroughputSequencing, Methylseq, RNAseq, Sequencing, Software
Version	2.17.0
In Bioconductor since	BioC 2.13 (R-3.0) (6 years)
License	GPL-2
Depends	R (>= 3.5.0), Rsamtools, GenomicFeatures(>= 1.14.5), rtracklayer, GenomicAlignments
Imports
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	exomePeak_2.17.0.tar.gz
Windows Binary	exomePeak_2.17.0.zip
Mac OS X 10.11 (El Capitan)	exomePeak_2.17.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/exomePeak
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/exomePeak
Package Short Url	https://bioconductor.org/packages/exomePeak/
Package Downloads Report	Download Stats