exomePeak
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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
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>
citation("exomePeak")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| An introduction to exomePeak | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | HighThroughputSequencing, Methylseq, RNAseq, Sequencing, Software |
| Version | 2.17.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.5.0), Rsamtools, GenomicFeatures(>= 1.14.5), rtracklayer, GenomicAlignments |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/exomePeak/ |
| Package Short Url | https://bioconductor.org/packages/exomePeak/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |