HiCDCPlus
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HiCDCPlus.
Hi-C Direct Caller Plus
Bioconductor version: 3.16
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("HiCDCPlus")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text |
Details
| biocViews | DNA3DStructure, HiC, Normalization, Software |
| Version | 1.6.0 |
| 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_1.6.0.tar.gz |
| Windows Binary | HiCDCPlus_1.6.0.zip |
| macOS Binary (x86_64) | HiCDCPlus_1.6.0.tgz |
| macOS Binary (arm64) | HiCDCPlus_1.6.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |