HiCDCPlus

DOI: 10.18129/B9.bioc.HiCDCPlus    

This is the development version of HiCDCPlus; to use it, please install the devel version of Bioconductor.

Hi-C Direct Caller Plus

Bioconductor version: Development (3.13)

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 "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews DNA3DStructure, HiC, Normalization, Software
Version 0.99.14
In Bioconductor since BioC 3.13 (R-4.1)
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
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
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package HiCDCPlus_0.99.14.tar.gz
Windows Binary HiCDCPlus_0.99.13.zip
macOS 10.13 (High Sierra) HiCDCPlus_0.99.14.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCDCPlus
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCDCPlus
Package Short Url https://bioconductor.org/packages/HiCDCPlus/
Package Downloads Report Download Stats

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