Package: UMI4Cats
Title: UMI4Cats: Processing, analysis and visualization of UMI-4C
        chromatin contact data
Version: 1.21.0
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 (>= 4.1.0), 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, annotate, rlang,
        GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics
Suggests: knitr, rmarkdown, BiocStyle, org.Hs.eg.db,
        TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
        tidyr, testthat
biocViews: QualityControl, Preprocessing, Alignment, Normalization,
        Visualization, Sequencing, Coverage
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Config/pak/sysreqs: make libmagick++-dev gsfonts libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:01:19 UTC
RemoteUrl: https://github.com/bioc/UMI4Cats
RemoteRef: HEAD
RemoteSha: f049a0a682f5853f3941bcbbbdae7814f17701c7
NeedsCompilation: no
Packaged: 2025-10-30 14:36:44 UTC; root
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 4.6.0; ; 2025-10-30 14:40:42 UTC; windows
