Package: exomePeak2
Type: Package
Title: Bias Awared Peak Calling and Quantification for MeRIP-Seq
Version: 1.0.0
Author: Zhen Wei
Maintainer: Zhen Wei <zhen.wei10@icloud.com>
Description: 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.
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,RMariaDB,methods,stats,utils,Biobase,GenomeInfoDb
Depends: SummarizedExperiment,cqn
biocViews: Sequencing, MethylSeq, RNASeq, ExomeSeq, Coverage,
        Normalization, Preprocessing, ImmunoOncology,
        DifferentialExpression
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.0.2
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/exomePeak2
git_branch: RELEASE_3_11
git_last_commit: 0b57ebf
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-27
NeedsCompilation: no
Packaged: 2020-04-28 04:42:59 UTC; biocbuild
Built: R 4.0.0; ; 2020-05-12 15:38:16 UTC; unix
