Package: UMI4Cats
Title: UMI4Cats: Processing, analysis and visualization of UMI-4C
        chromatin contact data
Version: 1.19.2
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 (>= 4.1.0), SummarizedExperiment
Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo,
        ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr,
        BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr,
        Rbowtie2, methods, GenomeInfoDb, GenomicAlignments,
        RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate,
        rlang, GenomicFeatures, BiocFileCache, rappdirs, fda,
        BiocGenerics
Suggests: knitr, rmarkdown, BiocStyle,
        TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
        tidyr, testthat
biocViews: QualityControl, Preprocessing, Alignment, Normalization,
        Visualization, Sequencing, Coverage
VignetteBuilder: knitr
RoxygenNote: 7.3.2
git_url: https://git.bioconductor.org/packages/UMI4Cats
git_branch: devel
git_last_commit: 96253ad
git_last_commit_date: 2025-09-23
Repository: Bioconductor 3.22
Date/Publication: 2025-09-23
NeedsCompilation: no
Packaged: 2025-09-23 21:59:15 UTC; biocbuild
Author: Mireia Ramos-Rodriguez [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8083-2445>),
  Marc Subirana-Granes [aut],
  Lorenzo Pasquali [aut]
Maintainer: Mireia Ramos-Rodriguez <mireiarr9@gmail.com>
Built: R 4.5.1; ; 2025-09-24 02:59:32 UTC; unix
