HiCDCPlus
This is thereleased version of HiCDCPlus; for the devel version, seeHiCDCPlus.
Hi-C Direct Caller Plus
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0003-3858-8332
Maintainer: Merve Sahin <merve.sahn at gmail.com>
citation("HiCDCPlus")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("HiCDCPlus")For older versions of R, please refer to the appropriateBioconductor 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 | 1.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | HiCDCPlus_1.18.0.tar.gz |
| Windows Binary (x86_64) | HiCDCPlus_1.18.0.zip (64-bit only) |
| macOS Binary (x86_64) | HiCDCPlus_1.18.0.tgz |
| macOS Binary (arm64) | HiCDCPlus_1.18.0.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 |