Package: HiCDCPlus
Type: Package
Title: Hi-C Direct Caller Plus
Version: 1.6.0
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
git_url: https://git.bioconductor.org/packages/HiCDCPlus
git_branch: RELEASE_3_16
git_last_commit: 65cf744
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
Packaged: 2022-11-02 00:54:35 UTC; biocbuild
Author: Merve Sahin [cre, aut] (<https://orcid.org/0000-0003-3858-8332>)
Maintainer: Merve Sahin <merve.sahn@gmail.com>
Built: R 4.2.1; x86_64-w64-mingw32; 2022-11-02 13:44:45 UTC; windows
ExperimentalWindowsRuntime: ucrt
Archs: x64
