Package: HiCDOC
Title: A/B compartment detection and differential analysis
Version: 1.0.0
Date: 2022-06-16
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, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats,
        S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, rhdf5,
        grid, ggpubr, gridExtra, ggExtra, data.table, multiHiCcompare,
        GenomeInfoDb
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager
RoxygenNote: 7.1.2
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_16
git_last_commit: 8b0d83d
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
NeedsCompilation: yes
Packaged: 2022-11-01 21:47:56 UTC; biocbuild
Author: Kurylo Cyril [aut],
  Zytnicki Matthias [aut],
  Foissac Sylvain [aut],
  Maigné Élise [aut, cre]
Maintainer: Maigné Élise <elise.maigne@inrae.fr>
Built: R 4.2.2; x86_64-conda-linux-gnu; 2022-11-08 00:12:12 UTC; unix
