HiCDCPlus

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 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNA3DStructure, HiC, Normalization, Software
Version	1.12.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 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

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_1.12.0.tar.gz
Windows Binary (x86_64)	HiCDCPlus_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	HiCDCPlus_1.12.0.tgz
macOS Binary (arm64)	HiCDCPlus_1.12.0.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