DESCRIPTION

Package: UMI4Cats
Title: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
Version: 1.13.0
Authors@R: c(
    person(given = "Mireia",
           family = "Ramos-Rodriguez",
           role = c("aut", "cre"),
           email = "mireiarr9@gmail.com",
           comment = c(ORCID = "0000-0001-8083-2445")),
    person(given = "Marc",
           family = "Subirana-Granes",
           role = c("aut"),
           email = "marc.subirana@upf.edu"),
    person(given = "Lorenzo",
           family = "Pasquali",
           role = c("aut"),
           email = "lorenzo.pasquali@upf.edu"))
URL: https://github.com/Pasquali-lab/UMI4Cats
Description: UMI-4C is a technique that allows characterization of 3D chromatin 
    interactions with a bait of interest, taking advantage of a sonication step to 
    produce unique molecular identifiers (UMIs) that help remove duplication 
    bias, thus allowing a better differential comparsion of chromatin 
    interactions between conditions. This package allows processing of UMI-4C 
    data, starting from FastQ files provided by the sequencing facility. It provides 
    two statistical methods for detecting differential contacts and includes a 
    visualization function to plot integrated information from a UMI-4C assay.
BugReports: https://github.com/Pasquali-lab/UMI4Cats/issues
License: Artistic-2.0
Encoding: UTF-8
Depends: 
    R (>= 4.0.0),
    SummarizedExperiment
Imports: 
    magick,
    cowplot,
    scales,
    GenomicRanges,
    ShortRead,
    zoo,
    ggplot2,
    reshape2,
    regioneR,
    IRanges,
    S4Vectors,
    magrittr,
    dplyr,
    BSgenome,
    Biostrings,
    DESeq2,
    R.utils,
    Rsamtools,
    stringr,
    Rbowtie2,
    methods,
    GenomeInfoDb,
    GenomicAlignments,
    RColorBrewer,
    utils,
    grDevices,
    stats,
    org.Hs.eg.db,
    annotate,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    rlang,
    GenomicFeatures,
    BiocFileCache,
    rappdirs,
    fda,
    BiocGenerics
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle,
    BSgenome.Hsapiens.UCSC.hg19,
    tidyr,
    testthat
biocViews:
    QualityControl,
    Preprocessing,
    Alignment,
    Normalization,
    Visualization,
    Sequencing,
    Coverage
VignetteBuilder: knitr
RoxygenNote: 7.1.1