Package: HiSpaR
Type: Package
Title: Hierarchical Inference of Spatial Positions from Hi-C Data
Version: 1.0.0
Date: 2026-01-15
Authors@R: c(
    person("Yingcheng", "Luo", email = "lyc22@mails.tsinghua.edu.cn", role = c("aut", "cre"))
    )
Description: 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.
License: MIT + file LICENSE
Depends: R (>= 4.5.0)
Imports: Rcpp (>= 1.0.0), utils, stats, Matrix, HiCExperiment
biocViews: Software, Epigenetics, HiC, StructuralPrediction, Bayesian,
        Spatial
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++17, GNU make, Armadillo (>= 9.0), OpenMP
URL: https://github.com/masterStormtrooper/HiSpaR
BugReports: https://github.com/masterStormtrooper/HiSpaR/issues
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.3
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rgl,
        HiContactsData, HiContacts, plotly, callr
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/HiSpaR
git_branch: RELEASE_3_23
git_last_commit: 4faeb40
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: yes
Packaged: 2026-04-28 22:40:19 UTC; biocbuild
Author: Yingcheng Luo [aut, cre]
Maintainer: Yingcheng Luo <lyc22@mails.tsinghua.edu.cn>
