Package: HiCDOC
Title: A/B compartment detection and differential analysis
Version: 1.13.0
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: devel
git_last_commit: 6ee95b8
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
