DOI: 10.18129/B9.bioc.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>

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biocViews Coverage, DifferentialExpression, ExomeSeq, ImmunoOncology, MethylSeq, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (0.5 years)
License GPL (>= 2)
Depends SummarizedExperiment, cqn
Imports Rsamtools, GenomicAlignments, GenomicRanges, GenomicFeatures, DESeq2, ggplot2, mclust, genefilter, Biostrings, BSgenome, BiocParallel, IRanges, S4Vectors, reshape2, rtracklayer, apeglm, RMariaDB, methods, stats, utils, Biobase, GenomeInfoDb
Suggests knitr, rmarkdown
BugReports https://github.com/ZW-xjtlu/exomePeak2/issues
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