HiCool
This is the released version of HiCool; for the devel version, see HiCool.
HiCool
Bioconductor version: Release (3.23)
HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.
Author: Jacques Serizay [aut, cre]
Maintainer: Jacques Serizay <jacquesserizay at gmail.com>
citation("HiCool")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiCool")
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("HiCool")| HiCool | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | DNA3DStructure, DataImport, HiC, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2), HiCExperiment |
| Imports | BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet, vroom, basilisk.utils, basilisk, reticulate, rmarkdown, rmdformats, plotly, dplyr, stringr, sessioninfo, utils |
| System Requirements | |
| URL | https://github.com/js2264/HiCool |
| Bug Reports | https://github.com/js2264/HiCool/issues |
See More
| Suggests | HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OHCA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HiCool_1.12.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | HiCool_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | HiCool_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HiCool |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiCool |
| Bioc Package Browser | https://code.bioconductor.org/browse/HiCool/ |
| Package Short Url | https://bioconductor.org/packages/HiCool/ |
| Package Downloads Report | Download Stats |