HiCDOC
This is the released version of HiCDOC; for the devel version, see HiCDOC.
A/B compartment detection and differential analysis
Bioconductor version: Release (3.20)
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>
Installation
To install this package, start R (version "4.4") 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 | 1.8.0 |
In Bioconductor since | BioC 3.16 (R-4.2) (2 years) |
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, grid, cowplot, gridExtra, data.table, multiHiCcompare, GenomeInfoDb |
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 | treediff |
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_1.8.0.tar.gz |
Windows Binary (x86_64) | HiCDOC_1.8.0.zip |
macOS Binary (x86_64) | HiCDOC_1.8.0.tgz |
macOS Binary (arm64) | HiCDOC_1.8.0.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 |