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HiCDCPlus

This is the development version of HiCDCPlus; for the stable release version, see HiCDCPlus.

Hi-C Direct Caller Plus


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HiCDCPlus")

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

Documentation

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

browseVignettes("HiCDCPlus")
Analyzing Hi-C and HiChIP data with HiCDCPlus HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNA3DStructure, HiC, Normalization, Software
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends
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+
URL
See More
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
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HiCDCPlus_1.11.0.tar.gz
Windows Binary HiCDCPlus_1.11.0.zip (64-bit only)
macOS Binary (x86_64) HiCDCPlus_1.11.0.tgz
macOS Binary (arm64) HiCDCPlus_1.11.0.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/
Package Downloads Report Download Stats