HiCBricks
This package is for version 3.8 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: 3.8
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]
Maintainer: Koustav Pal <koustav.pal at ifom.eu>
citation("HiCBricks")
):
Installation
To install this package, start R (version "3.5") 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")
HiCBricks | R Script | |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | DataImport, HiC, Infrastructure, Sequencing, Software, Technology |
Version | 1.0.0 |
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, BiocFileCache, rappdirs |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | HiCBricks_1.0.0.tar.gz |
Windows Binary | HiCBricks_1.0.0.zip |
Mac OS X 10.11 (El Capitan) | HiCBricks_1.0.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/HiCBricks |
Source Repository (Developer Access) | git clone [email protected]: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 3.8 | Source Archive |