DESCRIPTION

Package: surf
Type: Package
Title: Statistical Utility for RBP (RNA binding protein) Functions
Version: 0.99.1
Date: 2021-03-22
Authors@R: 
    person(given = "Fan",
           family = "Chen",
           role = c("aut", "cre"),
           email = "fan.chen@wisc.edu",
           comment = c(ORCID = "0000-0003-4508-6023"))
    person(given = "Sunduz",
           family = "Keles",
           role = c("aut", "cre"),
           email = "keles@stat.wisc.edu",
           comment = c(ORCID = "0000-0001-9048-0922"))
Description: 
    Advances in high-throughput profiling of RNA-binding proteins (RBPs) have 
    resulted in CLIP-seq datasets coupled with transcriptome profiling by 
    RNA-seq. However, analysis methods that integrate both types of data are 
    lacking. We describe SURF, Statistical Utility for RBP Functions, for 
    integrative analysis of large collections of CLIP-seq and RNA-seq data to 
    identify alternative splicing (AS), alternative transcription 
    initiation (ATI), and alternative polyadenylation (APA) events regulated by 
    individual RBPs and elucidate protein-RNA interactions governing these 
    events. 
URL: https:github.com/fchen365/surf
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 4.0),
    doParallel,
    DEXSeq
Imports:
    arm,
    stats,
    withr,
    rlang,
    dplyr,
    tidyr,
    doRNG,
    scales,
    ggpubr,
    Matrix,
    AUCell,
    IRanges,
    methods,
    stringr,
    ggplot2,
    foreach,
    parallel,
    reshape2,
    magrittr,
    Rsubread,
    S4Vectors,
    ensembldb,
    data.table,
    rtracklayer,
    BiocGenerics,
    BiocParallel,
    GenomicRanges,
    SummarizedExperiment,
Suggests:
    knitr,
    testthat,
    markdown,
    rmarkdown,
    BiocStyle,
Roxygen: 
    list(markdown = TRUE)
VignetteBuilder: knitr
biocViews: AlternativeSplicing, RNASeq, DNASeq, Sequencing, Transcription, 
   Visualization, Coverage, Alignment, DataImport
RoxygenNote: 7.1.1