Package: HiCDOC
Title: A/B compartment detection and differential analysis
Version: 1.14.0
Date: 2025-07-22
Authors@R: c(
    person("Kurylo", "Cyril", email = "cyril.kurylo@inrae.fr", role = c("aut")),
    person("Zytnicki", "Matthias", email = "matthias.zytnicki@inrae.fr", role = c("aut")),
    person("Foissac", "Sylvain", email = "sylvain.foissac@inrae.fr", role = c("aut")),
    person("Maigné", "Élise", email = "elise.maigne@inrae.fr", role = c("aut", "cre")))
Description: 
    HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning
    to predict A/B compartments from multiple replicates, and detects
    significant compartment changes between experiment conditions.
    It provides a collection of functions assembled into a pipeline to filter 
    and normalize the data, predict the compartments and visualize the results. 
    It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or 
    `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.
License: LGPL-3
Encoding: UTF-8
SystemRequirements: C++11
Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>=
        4.1.0)
Imports: methods, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools,
        pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra,
        data.table, multiHiCcompare, Seqinfo
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5
RoxygenNote: 7.3.2
biocViews: HiC, DNA3DStructure, Normalization, Sequencing, Software,
        Clustering
VignetteBuilder: knitr
URL: https://github.com/mzytnicki/HiCDOC
BugReports: https://github.com/mzytnicki/HiCDOC/issues
git_url: https://git.bioconductor.org/packages/HiCDOC
git_branch: RELEASE_3_23
git_last_commit: f610dc0
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: yes
Packaged: 2026-04-28 22:37:22 UTC; biocbuild
Author: Kurylo Cyril [aut],
  Zytnicki Matthias [aut],
  Foissac Sylvain [aut],
  Maigné Élise [aut, cre]
Maintainer: Maigné Élise <elise.maigne@inrae.fr>
