Type: Package
Package: richCluster
Title: Fast, Robust Clustering Algorithms for Gene Enrichment Data
Version: 2.0.1
Date: 2026-09-18
Authors@R: c(
    person("Junguk", "Hur", , "hurlabshared@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0736-2149")),
    person("Sarah", "Hong", role = "aut"),
    person("Jane", "Kim", role = "aut")
  )
Maintainer: Junguk Hur <hurlabshared@gmail.com>
Description: Clusters functionally related biological terms from gene
        set enrichment results. Terms are compared by the overlap of
        their gene sets using Cohen's kappa, the Jaccard index, or the
        Dice coefficient, and the resulting similarity matrix is
        grouped either by agglomerative hierarchical clustering with
        single, complete, average, or Ward linkage, or by the
        seed-and-merge procedure of the 'DAVID' functional
        classification tool. The distance and clustering routines are
        written in 'C++' for speed. The methods are described in Huang
        et al. (2007) <doi:10.1186/gb-2007-8-9-r183>, Ward (1963)
        <doi:10.1080/01621459.1963.10500845>, Cohen (1960)
        <doi:10.1177/001316446002000104>, and Jaccard (1912)
        <doi:10.1111/j.1469-8137.1912.tb05611.x>.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: dplyr, fields, heatmaply, igraph, magrittr, networkD3, plotly,
        Rcpp (>= 1.0.14), stats, tidyr, viridis
Suggests: devtools, knitr, rmarkdown, roxygen2, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
URL: https://github.com/hurlab/richCluster
BugReports: https://github.com/hurlab/richCluster/issues
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.0.0
NeedsCompilation: yes
Packaged: 2026-10-31 07:22:59 UTC; root
Author: Junguk Hur [aut, cre] (ORCID:
        <https://orcid.org/0000-0002-0736-2149>), Sarah Hong [aut],
        Jane Kim [aut]
Config/pak/sysreqs: cmake libglpk-dev make libmagick++-dev gsfonts
        libicu-dev libuv1-dev libxml2-dev libssl-dev
Repository: https://hurlab.r-universe.dev
Date/Publication: 2026-09-30 22:21:18 UTC
RemoteUrl: https://github.com/hurlab/richcluster
RemoteRef: HEAD
RemoteSha: a0d1f630fbe64089ab38516116b78962672e6349