Type: Package
Package: HicAggR
Title: Set of 3D genomic interaction analysis tools
Version: 1.6.0
Authors@R: c(
    person("Robel", "Tesfaye", email = "rob.tesf@gmail.com",
        role = c("aut","ctb"), comment = c(ORCID="0000-0003-2358-219X")),
    person("David", "Depierre", email = "dav.depierre@gmail.com",
        role = "aut"),
    person("Naomi", "Schickele", email = "naomi.schickele@univ-tlse3.fr",
        role = "ctb"),
    person("Nicolas", "Chanard", email = "nico.chanard@gmail.com",
        role = "aut"),
    person("Refka", "Askri", email = "refka.askri@univ-tlse3.fr",
        role = "ctb"),
    person("Stéphane", "Schaak", email = "stephane.schaak@inserm.fr",
        role = c("aut","ctb")),
    person("Pascal", "Martin", email = "pascal.martin@inra.fr",
        role = "ctb"),
    person("Olivier", "Cuvier", email = "olivier.cuvier@univ-tlse3.fr",
        role = c("cre","ctb"), comment = c(ORCID="0000-0003-0644-2734"))
    )
Description: This package provides a set of functions useful in the
        analysis of 3D genomic interactions. It includes the import of
        standard HiC data formats into R and HiC normalisation
        procedures. The main objective of this package is to improve
        the visualization and quantification of the analysis of HiC
        contacts through aggregation. The package allows to import 1D
        genomics data, such as peaks from ATACSeq, ChIPSeq, to create
        potential couples between features of interest under
        user-defined parameters such as distance between pairs of
        features of interest. It allows then the extraction of contact
        values from the HiC data for these couples and to perform
        Aggregated Peak Analysis (APA) for visualization, but also to
        compare normalized contact values between conditions. Overall
        the package allows to integrate 1D genomics data with 3D
        genomics data, providing an easy access to HiC contact values.
biocViews: Software, HiC, DataImport, DataRepresentation,
        Normalization, Visualization, DNA3DStructure, ATACSeq, ChIPSeq,
        DNaseSeq, RNASeq
License: MIT + file LICENSE
URL: https://bioconductor.org/packages/HicAggR,
        https://cuvierlab.github.io/HicAggR/,
        https://github.com/CuvierLab/HicAggR
BugReports: https://github.com/CuvierLab/HicAggR/issues
Depends: R (>= 4.2.0)
Imports: InteractionSet, BiocGenerics, BiocParallel, dplyr, Seqinfo,
        GenomicRanges, ggplot2, grDevices, IRanges, Matrix, methods,
        rhdf5, rlang, rtracklayer, S4Vectors, stats, utils, strawr,
        tibble, stringr, tidyr, gridExtra, data.table, reshape,
        checkmate, purrr, withr
Suggests: GenomeInfoDb, covr, tools, kableExtra (>= 1.3.4), knitr (>=
        1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache (>= 2.6.1)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:30:21 UTC
RemoteUrl: https://github.com/bioc/HicAggR
RemoteRef: RELEASE_3_22
RemoteSha: 8551a70db58f66d372d0f35eb6f3e3cc816a8608
NeedsCompilation: no
Packaged: 2026-02-28 08:27:50 UTC; root
Author: Robel Tesfaye [aut, ctb] (ORCID:
    <https://orcid.org/0000-0003-2358-219X>),
  David Depierre [aut],
  Naomi Schickele [ctb],
  Nicolas Chanard [aut],
  Refka Askri [ctb],
  Stéphane Schaak [aut, ctb],
  Pascal Martin [ctb],
  Olivier Cuvier [cre, ctb] (ORCID:
    <https://orcid.org/0000-0003-0644-2734>)
Maintainer: Olivier Cuvier <olivier.cuvier@univ-tlse3.fr>
Built: R 4.5.2; ; 2026-02-28 08:29:49 UTC; windows
