To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("exomePeak")

In most cases, you don't need to download the package archive at all.

exomePeak

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

Bioconductor version: Release (3.0)

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: Jia Meng <jia.meng at xjtlu.edu.cn>

Maintainer: Jia Meng <jia.meng at xjtlu.edu.cn>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("exomePeak")

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 1.6.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-2
Depends Rsamtools, GenomicFeatures(>= 1.14.5), rtracklayer
Imports
Suggests
System Requirements
URL
Depends On Me
Imports Me
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Package Archives

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

Package Source exomePeak_1.6.0.tar.gz
Windows Binary exomePeak_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) exomePeak_1.6.0.tgz
Mac OS X 10.9 (Mavericks) exomePeak_1.6.0.tgz
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