Type: Package
Package: HicAggR
Title: Set of 3D genomic interaction analysis tools
Version: 0.99.4
Authors@R: c(
    person("Nicolas", "Chanard", email = "nico.chanard@gmail.com",
        role = "aut"),
    person("David", "Depierre", email = "dav.depierre@gmail.com",
        role = "aut"),
    person("Robel", "Tesfaye", email = "rob.tesf@gmail.com",
        role = c("aut","ctb"), comment = c(ORCID="0000-0003-2358-219X")),
    person("Naomi", "Schickele", email = "naomi.schickele@univ-tlse3.fr",
        role = "ctb"),
    person("Refka", "Askri", email = "refka.askri@univ-tlse3.fr",
        role = "ctb"),
    person("Pascal", "Martin", email = "pascal.martin@inra.fr",
        role = "ctb"),
    person("Stephane", "Schaak", email = "stephane.schaak@inserm.fr",
        role = c("aut","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://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,
        GenomeInfoDb, GenomicRanges, ggplot2, grDevices, IRanges,
        Matrix, methods, rhdf5, rlang, rtracklayer, S4Vectors, stats,
        utils, strawr, tibble, stringr, tidyr, gridExtra, data.table,
        reshape
Suggests: covr, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
NeedsCompilation: no
Packaged: 2024-03-28 15:51:57 UTC; pkgbuild
Author: Nicolas Chanard [aut],
  David Depierre [aut],
  Robel Tesfaye [aut, ctb] (<https://orcid.org/0000-0003-2358-219X>),
  Naomi Schickele [ctb],
  Refka Askri [ctb],
  Pascal Martin [ctb],
  Stephane Schaak [aut, ctb],
  Olivier Cuvier [cre, ctb] (<https://orcid.org/0000-0003-0644-2734>)
Maintainer: Olivier Cuvier <olivier.cuvier@univ-tlse3.fr>
