Package: hicream
Title: HIC diffeREntial Analysis Method
Version: 0.0.4
Date: 2026-01-30
Maintainer: Elise Jorge <elise.jorge@inrae.fr>
Authors@R: c(
    person("Elise", "Jorge", , "elise.jorge@inrae.fr", role = c("aut", "cre")),
    person("Sylvain", "Foissac", , "sylvain.foissac@inrae.fr", role = "aut",
           comment = c(ORCID = "0000-0002-2631-5356")),
    person("Toby", "Hocking", , "toby.hocking@r-project.org", role = "aut",
           comment = c(ORCID = "0000-0002-3146-0865")),
    person("Pierre", "Neuvial", , "pierre.neuvial@math.univ-toulouse.fr", 
           role = "aut", comment = c(ORCID = "0000-0003-3584-9998")),
    person("Nathalie", "Vialaneix", , "nathalie.vialaneix@inrae.fr", 
           role = "aut", comment = c(ORCID = "0000-0003-1156-0639")),
    person("Gilles", "Blanchard", role = "ctb"), 
    person("Guillermo", "Durand", role= "ctb", 
           comment = c(ORCID = "0000-0003-4056-5631")),
    person("Nicolas", "Enjalbert-Courrech", role = "ctb"),
    person("Etienne", "Roquain", role = "ctb")
  )
Description: Perform Hi-C data differential analysis based on pixel-level
    differential analysis and a post hoc inference strategy to quantify
    signal in clusters of pixels. Clusters of pixels are obtained through
    a connectivity-constrained two-dimensional hierarchical clustering.
License: GPL (>= 3)
URL: https://scales.pages-forge.inrae.fr/hicream/,
        https://forge.inrae.fr/scales/hicream
BugReports: https://forge.inrae.fr/scales/hicream/-/issues
Depends: R (>= 4.0.0), reticulate
SystemRequirements: Python (>= 3.9)
Imports: adjclust, auk, BiocGenerics, csaw, diffHic, dplyr, edgeR,
        GenomeInfoDb, GenomicRanges, InteractionSet, limma, Matrix,
        methods, reshape2, rlang, S4Vectors, stats,
        SummarizedExperiment, utils, viridis
Suggests: knitr, rmarkdown
Encoding: UTF-8
RoxygenNote: 7.3.3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-01-30 15:01:53 UTC; nathalie
Author: Elise Jorge [aut, cre],
  Sylvain Foissac [aut] (ORCID: <https://orcid.org/0000-0002-2631-5356>),
  Toby Hocking [aut] (ORCID: <https://orcid.org/0000-0002-3146-0865>),
  Pierre Neuvial [aut] (ORCID: <https://orcid.org/0000-0003-3584-9998>),
  Nathalie Vialaneix [aut] (ORCID:
    <https://orcid.org/0000-0003-1156-0639>),
  Gilles Blanchard [ctb],
  Guillermo Durand [ctb] (ORCID: <https://orcid.org/0000-0003-4056-5631>),
  Nicolas Enjalbert-Courrech [ctb],
  Etienne Roquain [ctb]
Repository: CRAN
Date/Publication: 2026-01-30 15:50:02 UTC
Built: R 4.6.0; ; 2026-04-26 18:59:39 UTC; unix
