HiCDOC
This is the released version of HiCDOC; for the devel version, see HiCDOC.
A/B compartment detection and differential analysis
Bioconductor version: Release (3.23)
HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.
Author: Kurylo Cyril [aut], Zytnicki Matthias [aut], Foissac Sylvain [aut], Maigné Élise [aut, cre]
Maintainer: Maigné Élise <elise.maigne at inrae.fr>
citation("HiCDOC")):
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")
BiocManager::install("HiCDOC")
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("HiCDOC")| HiCDOC | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DNA3DStructure, HiC, Normalization, Sequencing, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | LGPL-3 |
| Depends | InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) |
| Imports | methods, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, Seqinfo |
| System Requirements | C++11 |
| URL | https://github.com/mzytnicki/HiCDOC |
| Bug Reports | https://github.com/mzytnicki/HiCDOC/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 |
| Linking To | Rcpp |
| Enhances | |
| 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 | HiCDOC_1.14.0.tar.gz |
| Windows Binary (x86_64) | HiCDOC_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | HiCDOC_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | HiCDOC_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HiCDOC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiCDOC |
| Bioc Package Browser | https://code.bioconductor.org/browse/HiCDOC/ |
| Package Short Url | https://bioconductor.org/packages/HiCDOC/ |
| Package Downloads Report | Download Stats |