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 Config/pak/sysreqs: libssl-dev zlib1g-dev Repository: Bioconductor 3.23 Date/Publication: 2026-04-28 12:58:38 UTC RemoteUrl: https://github.com/bioc/HiCDOC RemoteRef: RELEASE_3_23 RemoteSha: f610dc04c2877d741d9b0bda44b4f22d1f3259f3 NeedsCompilation: yes Packaged: 2026-11-01 18:16:07 UTC; root Author: Kurylo Cyril [aut], Zytnicki Matthias [aut], Foissac Sylvain [aut], Maigné Élise [aut, cre] Maintainer: Maigné Élise