DOI: 10.18129/B9.bioc.exomePeak2    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see exomePeak2.

Bias-aware Peak Calling and Quantification for MeRIP-Seq

Bioconductor version: 3.13

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>

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biocViews Coverage, DifferentialExpression, ExomeSeq, MethylSeq, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version 1.4.2
In Bioconductor since BioC 3.11 (R-4.0) (1.5 years)
License GPL (>= 2)
Depends 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
Suggests knitr, rmarkdown, RMariaDB
BugReports https://github.com/ZW-xjtlu/exomePeak2/issues
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