Package: HiCDCPlus
Type: Package
Title: Hi-C Direct Caller Plus
Version: 1.21.0
Description: Systematic 3D interaction calls and differential analysis
        for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller
        plus) package enables principled statistical analysis of Hi-C
        and HiChIP data sets – including calling significant
        interactions within a single experiment and performing
        differential analysis between conditions given replicate
        experiments – to facilitate global integrative studies. HiC-DC+
        estimates significant interactions in a Hi-C or HiChIP
        experiment directly from the raw contact matrix for each
        chromosome up to a specified genomic distance, binned by
        uniform genomic intervals or restriction enzyme fragments, by
        training a background model to account for random polymer
        ligation and systematic sources of read count variation.
Authors@R: person("Merve", "Sahin", email="merve.sahn@gmail.com", role=c("cre","aut"), comment=c(ORCID = "0000-0003-3858-8332"))
License: GPL-3
Encoding: UTF-8
biocViews: HiC, DNA3DStructure, Software, Normalization
RoxygenNote: 7.1.1
SystemRequirements: JRE 8+
LinkingTo: Rcpp
Imports:
        Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors
Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10,
        BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
        RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix,
        BiocFileCache, rappdirs
Enhances: parallel
VignetteBuilder: knitr
NeedsCompilation: yes
Config/pak/sysreqs: cmake libglpk-dev make libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:55:01 UTC
RemoteUrl: https://github.com/bioc/HiCDCPlus
RemoteRef: HEAD
RemoteSha: be86a097c5b832816450744455b97f2f03e0a9aa
Packaged: 2026-07-04 23:10:47 UTC; root
Author: Merve Sahin [cre, aut] (ORCID: <https://orcid.org/0000-0003-3858-8332>)
Maintainer: Merve Sahin <merve.sahn@gmail.com>