exomePeak2
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see exomePeak2.
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bioconductor version: 3.11
exomePeak2 provides bias awared quantification and peak detection on Methylated RNA immunoprecipitation sequencing data (MeRIP-Seq). MeRIP-Seq is a commonly applied sequencing technology to measure the transcriptome-wide location and abundance of RNA modification sites under a given cellular condition. However, the quantification and peak calling in MeRIP-Seq are sensitive to PCR amplification bias which is prevalent in next generation sequencing (NGS) techniques. In addition, the RNA-Seq based count data exhibits biological variation in small reads count. exomePeak2 collectively address these challanges by introducing a rich set of robust data science models tailored for MeRIP-Seq. With exomePeak2, users can perform peak calling, modification site quantification, and differential analysis with a straightforward one-step function. Alternatively, users could define personalized methods for their own analysis through multi-step functions and diagnostic plots.
Author: Zhen Wei
Maintainer: Zhen Wei <zhen.wei10 at icloud.com>
citation("exomePeak2")):
Installation
To install this package, start R (version "4.0") 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, ImmunoOncology, MethylSeq, Normalization, Preprocessing, RNASeq, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL (>= 2) |
| Depends | SummarizedExperiment, cqn |
| Imports | Rsamtools, GenomicAlignments, GenomicRanges, GenomicFeatures, DESeq2, ggplot2, mclust, genefilter, Biostrings, BSgenome, BiocParallel, IRanges, S4Vectors, reshape2, rtracklayer, apeglm, RMariaDB, methods, stats, utils, Biobase, GenomeInfoDb |
| 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 | exomePeak2_1.0.0.tar.gz |
| Windows Binary | exomePeak2_1.0.0.zip |
| macOS 10.13 (High Sierra) | exomePeak2_1.0.0.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 3.11 | Source Archive |