HiCDCPlus
This is the development version of HiCDCPlus; for the stable release version, see HiCDCPlus.
Hi-C Direct Caller Plus
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | DNA3DStructure, HiC, Normalization, Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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
Follow Installation instructions to use this package in your R session.
| Source Package | HiCDCPlus_1.21.0.tar.gz |
| Windows Binary (x86_64) | HiCDCPlus_1.21.0.zip |
| macOS Binary (big-sur-x86_64) | HiCDCPlus_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | HiCDCPlus_1.21.0.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 |