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Hi-C Direct Caller Plus

Bioconductor version: Release (3.19)

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.

Author: Merve Sahin [cre, aut]

Maintainer: Merve Sahin <merve.sahn at>

Citation (from within R, enter citation("HiCDCPlus")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Analyzing Hi-C and HiChIP data with HiCDCPlus HTML R Script
Reference Manual PDF


biocViews DNA3DStructure, HiC, Normalization, Software
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Imports Rcpp, InteractionSet, GenomicInteractions, bbmle, pscl, BSgenome, data.table, dplyr, tidyr, GenomeInfoDb, rlang, splines, MASS, GenomicRanges, IRanges, tibble, R.utils, Biostrings, rtracklayer, methods, S4Vectors
System Requirements JRE 8+
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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
Linking To Rcpp
Enhances parallel
Depends On Me
Imports Me
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Follow Installation instructions to use this package in your R session.

Source Package HiCDCPlus_1.12.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) HiCDCPlus_1.12.0.tgz
macOS Binary (arm64) HiCDCPlus_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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