HiSpaR
This is the released version of HiSpaR; for the devel version, see HiSpaR.
Hierarchical Inference of Spatial Positions from Hi-C Data
Bioconductor version: Release (3.23)
Provides R bindings for HiSpa, a hierarchical Bayesian model for inferring three-dimensional chromatin structures from Hi-C contact matrices using Markov Chain Monte Carlo (MCMC) sampling. The package implements a cluster-based hierarchical approach that efficiently handles large-scale Hi-C datasets. It uses Rcpp and RcppArmadillo for efficient C++ integration with the original HiSpa C++ implementation, enabling fast computation of chromatin structure inference through parallel MCMC sampling.
Author: Yingcheng Luo [aut, cre]
Maintainer: Yingcheng Luo <lyc22 at mails.tsinghua.edu.cn>
citation("HiSpaR")):Yingcheng Luo. HiSpaR: Hierarchical Inference of Spatial Positions from Hi-C Data. doi:10.18129/B9.bioc.HiSpaR, R package version 1.0.0, https://bioconductor.org/packages/HiSpaR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiSpaR")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("HiSpaR")| Getting Started with HiSpaR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, Epigenetics, HiC, Software, Spatial, StructuralPrediction |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | Rcpp (>= 1.0.0), utils, stats, Matrix, HiCExperiment |
| System Requirements | C++17, GNU make, Armadillo (>= 9.0), OpenMP |
| URL | https://github.com/masterStormtrooper/HiSpaR |
| Bug Reports | https://github.com/masterStormtrooper/HiSpaR/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rgl, HiContactsData, HiContacts, plotly, callr |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HiSpaR_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | HiSpaR_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | HiSpaR_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HiSpaR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiSpaR |
| Package Short Url | https://bioconductor.org/packages/HiSpaR/ |
| Package Downloads Report | Download Stats |