DOI: 10.18129/B9.bioc.HiCDCPlus  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see HiCDCPlus.

Hi-C Direct Caller Plus

Bioconductor version: 3.17

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 gmail.com>

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HTML R Script Analyzing Hi-C and HiChIP data with HiCDCPlus
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biocViews DNA3DStructure, HiC, Normalization, Software
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2.5 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
LinkingTo Rcpp
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
SystemRequirements JRE 8+
Enhances parallel
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package HiCDCPlus_1.8.0.tar.gz
Windows Binary HiCDCPlus_1.8.0.zip
macOS Binary (x86_64) HiCDCPlus_1.8.0.tgz
macOS Binary (arm64) HiCDCPlus_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCDCPlus
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCDCPlus
Bioc Package Browser https://code.bioconductor.org/browse/HiCDCPlus/
Package Short Url https://bioconductor.org/packages/HiCDCPlus/
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