HiCParser
This is the released version of HiCParser; for the devel version, see HiCParser.
Parser for HiC data in R
Bioconductor version: Release (3.23)
This package is a parser to import HiC data into R. It accepts several type of data: tabular files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files. The HiC data can be several files, for several replicates and conditions. The data is formated in an InteractionSet object.
Author: Zytnicki Matthias [aut], Maigné Élise [aut, cre]
Maintainer: Maigné Élise <elise.maigne at inrae.fr>
citation("HiCParser")):
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("HiCParser")
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("HiCParser")| Introduction to HiCParser | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, HiC, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | LGPL |
| Depends | |
| Imports | data.table, InteractionSet, GenomicRanges, SummarizedExperiment, Rcpp (>= 1.0.12), S4Vectors, gtools, pbapply, BiocGenerics, Seqinfo |
| System Requirements | |
| URL | https://github.com/emaigne/HiCParser |
| Bug Reports | https://github.com/emaigne/HiCParser/issues |
See More
| Suggests | rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) |
| 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 | HiCParser_1.4.0.tar.gz |
| Windows Binary (x86_64) | HiCParser_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | HiCParser_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | HiCParser_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HiCParser |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiCParser |
| Bioc Package Browser | https://code.bioconductor.org/browse/HiCParser/ |
| Package Short Url | https://bioconductor.org/packages/HiCParser/ |
| Package Downloads Report | Download Stats |