Type: Package
Package: richCluster
Title: Fast, Robust Clustering Algorithms for Gene Enrichment Data
Version: 2.0.0
Date: 2026-09-15
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
Config/roxygen2/version: 8.0.0
NeedsCompilation: yes
Packaged: 2026-09-16 20:23:18 UTC; juhur
Author: Junguk Hur [aut, cre] (ORCID: <https://orcid.org/0000-0002-0736-2149>),
  Sarah Hong [aut],
  Jane Kim [aut]
Repository: CRAN
Date/Publication: 2026-09-16 23:30:15 UTC
