HiCBricks
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see HiCBricks.
Framework for Storing and Accessing Hi-C Data Through HDF Files
Bioconductor version: 3.12
HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization.
Author: Koustav Pal [aut, cre], Carmen Livi [ctb], Ilario Tagliaferri [ctb]
Maintainer: Koustav Pal <koustav.pal at ifom.eu>
citation("HiCBricks")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiCBricks")
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("HiCBricks")| IntroductionToHiCBricks.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, HiC, Infrastructure, Sequencing, Software, Technology |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6), utils, curl, rhdf5, R6, grid |
| Imports | ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| 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 | HiCBricks_1.8.0.tar.gz |
| Windows Binary | HiCBricks_1.8.0.zip |
| macOS 10.13 (High Sierra) | HiCBricks_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HiCBricks |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiCBricks |
| Bioc Package Browser | https://code.bioconductor.org/browse/HiCBricks/ |
| Package Short Url | https://bioconductor.org/packages/HiCBricks/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |