Package: exomePeak2
Type: Package
Title: Bias-aware Peak Calling and Quantification for MeRIP-Seq
Version: 1.6.0
Authors@R: person("Zhen", "Wei", email = "zhen.wei10@icloud.com",
                  role = c("aut", "cre"))
Description: 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.
License: GPL (>= 2)
BugReports: https://github.com/ZW-xjtlu/exomePeak2/issues
Imports:
        Rsamtools,GenomicAlignments,GenomicRanges,GenomicFeatures,DESeq2,ggplot2,mclust,genefilter,Biostrings,BSgenome,BiocParallel,IRanges,S4Vectors,reshape2,rtracklayer,apeglm,methods,stats,utils,Biobase,GenomeInfoDb,BiocGenerics
Depends: SummarizedExperiment,cqn
biocViews: Sequencing, MethylSeq, RNASeq, ExomeSeq, Coverage,
        Normalization, Preprocessing, DifferentialExpression
Encoding: UTF-8
RoxygenNote: 7.1.0
Suggests: knitr, rmarkdown, RMariaDB
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/exomePeak2
git_branch: RELEASE_3_14
git_last_commit: 50ec4d5
git_last_commit_date: 2021-10-26
Date/Publication: 2021-10-26
NeedsCompilation: no
Packaged: 2021-10-26 21:26:21 UTC; biocbuild
Author: Zhen Wei [aut, cre]
Maintainer: Zhen Wei <zhen.wei10@icloud.com>
Built: R 4.1.1; ; 2021-11-08 12:37:19 UTC; unix
