HiCDOC
A/B compartment detection and differential analysis
Bioconductor version: Release (3.17)
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")):
Installation
To install this package, start R (version "4.3") 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 | 1.2.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (1 year) |
| License | LGPL (>= 3) |
| Depends | InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) |
| Imports | methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, rhdf5, grid, ggpubr, gridExtra, ggExtra, data.table, multiHiCcompare, GenomeInfoDb |
| Linking To | Rcpp |
| Suggests | knitr, rmarkdown, testthat, BiocStyle, BiocManager |
| System Requirements | C++11 |
| Enhances | |
| URL | https://github.com/mzytnicki/HiCDOC |
| Bug Reports | https://github.com/mzytnicki/HiCDOC/issues |
See More
| Depends On Me | |
| Imports Me | treediff |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HiCDOC_1.2.0.tar.gz |
| Windows Binary | HiCDOC_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | HiCDOC_1.2.0.tgz |
| macOS Binary (arm64) | HiCDOC_1.2.0.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 |