exomePeak2
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see exomePeak2.
Bias-aware Peak Calling and Quantification for MeRIP-Seq
Bioconductor version: 3.14
exomePeak2 provides bias-aware quantification and peak detection for Methylated RNA immunoprecipitation sequencing data (MeRIP-Seq). MeRIP-Seq is a commonly applied sequencing technology that can measure the location and abundance of RNA modification sites under given cell line conditions. However, quantification and peak calling in MeRIP-Seq are sensitive to PCR amplification biases, which generally present in next-generation sequencing (NGS) technologies. In addition, the count data generated by RNA-Seq exhibits significant biological variations between biological replicates. exomePeak2 collectively address the challenges by introducing a series of robust data science tools tailored for MeRIP-Seq. Using exomePeak2, users can perform peak calling, modification site quantification and differential analysis through a straightforward single-step function. Alternatively, multi-step functions can be used to generate diagnostic plots and perform customized analyses.
Author: Zhen Wei [aut, cre]
Maintainer: Zhen Wei <zhen.wei10 at icloud.com>
citation("exomePeak2")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, ExomeSeq, MethylSeq, Normalization, Preprocessing, RNASeq, Sequencing, Software |
| Version | 1.6.1 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5.0), SummarizedExperiment, cqn |
| Imports | Rsamtools, GenomicAlignments, GenomicRanges, GenomicFeatures, DESeq2, ggplot2, mclust, genefilter, Biostrings, BSgenome, BiocParallel, IRanges, S4Vectors, reshape2, rtracklayer, apeglm, methods, stats, utils, Biobase, GenomeInfoDb, BiocGenerics |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/ZW-xjtlu/exomePeak2/issues |
See More
| Suggests | knitr, rmarkdown, RMariaDB |
| 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_1.6.1.tar.gz |
| Windows Binary | exomePeak2_1.6.1.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | exomePeak2_1.6.1.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 3.14 | Source Archive |