exomePeak2
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This is the development version of exomePeak2; for the stable release version, see exomePeak2.
Peak Calling and differential analysis for MeRIP-Seq
Bioconductor version: Development (3.19)
exomePeak2 provides peak detection and differential methylation for Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) data. MeRIP-Seq is a commonly applied sequencing assay that measures the location and abundance of RNA modification sites under specific cellular conditions. In practice, the technique is sensitive to PCR amplification biases commonly found in NGS data. In addition, the efficiency of immunoprecipitation often varies between different IP samples. exomePeak2 can perform peak calling and differential analysis independent of GC content bias and IP efficiency changes.
Author: Zhen Wei [aut, cre]
Maintainer: Zhen Wei <zhen.wei10 at icloud.com>
citation("exomePeak2")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("exomePeak2")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Coverage, DifferentialMethylation, DifferentialPeakCalling, MethylSeq, PeakDetection, RNASeq, Sequencing, Software |
| Version | 1.15.1 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), SummarizedExperiment |
| Imports | Rsamtools, GenomicAlignments, GenomicRanges, GenomicFeatures, DESeq2, ggplot2, mclust, BSgenome, Biostrings, GenomeInfoDb, BiocParallel, IRanges, S4Vectors, rtracklayer, methods, stats, utils, BiocGenerics, magrittr, speedglm, splines |
| 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 | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/exomePeak2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/exomePeak2 |
| Package Short Url | https://bioconductor.org/packages/exomePeak2/ |
| Package Downloads Report | Download Stats |