HiSpaR
Hierarchical Inference of Spatial Positions from Hi-C Data
Bioconductor version: 3.24 · Package version: 1.1.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiSpaR")Details
| Maintainer | Yingcheng Luo <lyc22@mails.tsinghua.edu.cn> |
| Author | Yingcheng Luo [aut, cre] |
| License | MIT + file LICENSE |
| URL | https://github.com/masterStormtrooper/HiSpaR |
| Bug Reports | https://github.com/masterStormtrooper/HiSpaR/issues |
| System Requirements | C++17, GNU make, Armadillo (>= 9.0), OpenMP |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, Epigenetics, HiC, Software, Spatial, StructuralPrediction |
| Package Short Url | https://bioconductor.org/packages/HiSpaR/ |
Citation
From within R, enter citation("HiSpaR"):
Yingcheng Luo. HiSpaR: Hierarchical Inference of Spatial Positions from Hi-C Data. doi:10.18129/B9.bioc.HiSpaR, R package version 1.1.0, https://bioconductor.org/packages/HiSpaR.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | HiSpaR_1.1.0.tar.gz |
| macOS binary (arm64) | HiSpaR_1.1.0.tgz |
| macOS binary (x86_64) | HiSpaR_1.1.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: Rcpp (>= 1.0.0), utils, stats, Matrix, HiCExperiment
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rgl, HiContactsData, HiContacts, plotly, callr