2021-02-07

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.

To install exomePeak2 from Github, type the following command in R consel.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("SummarizedExperiment","cqn","Rsamtools",
                       "GenomicAlignments","GenomicRanges","GenomicFeatures",
                       "DESeq2","ggplot2","mclust",
                       "genefilter","BSgenome","BiocParallel",
                       "IRanges","S4Vectors","quantreg",
                       "reshape2","rtracklayer","apeglm","RMariaDB"))

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("ZW-xjtlu/exomePeak2", build_vignettes = TRUE)

To view the documentation of exomePeak2, type browseVignettes("exomePeak2") after installation.