HiCBricks
This package is for version 3.9 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: 3.9
A flexible framework for storing and accessing high-resolution Hi-C data through HDF files. HiCBricks allows import of Hi-C data through various formats such as the 2D matrix format or a generalized n-column table formats. In terms of access, HiCBricks offers functions to retrieve values from genomic loci separated by a certain distance, or the ability to fetch matrix subsets using word alike terms. HiCBricks will at a later point offer the ability to fetch multiple matrix subsets using fewer calls. It offers the capacity to store GenomicRanges that may be associated to a particular Hi-C experiment, to do basic ranges overlap (any, within) with the Hi-C experiment associated Ranges object and also to store any metadata that users may think to be relevant for their Hi-C experiment. Finally, you can do TAD calls with LSD and create pretty heatmaps.
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 "3.6") 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 | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5), utils, curl, rhdf5, R6, grid |
| Imports | ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest |
| 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_1.2.0.tar.gz |
| Windows Binary | HiCBricks_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | HiCBricks_1.2.0.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 3.9 | Source Archive |