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This is the development version of HGC; for the stable release version, see HGC.

A fast hierarchical graph-based clustering method

Bioconductor version: Development (3.20)

HGC (short for Hierarchical Graph-based Clustering) is an R package for conducting hierarchical clustering on large-scale single-cell RNA-seq (scRNA-seq) data. The key idea is to construct a dendrogram of cells on their shared nearest neighbor (SNN) graph. HGC provides functions for building graphs and for conducting hierarchical clustering on the graph. The users with old R version could visit to get HGC package built for R 3.6.

Author: Zou Ziheng [aut], Hua Kui [aut], XGlab [cre, cph]

Maintainer: XGlab <xglab at>

Citation (from within R, enter citation("HGC")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

HGC package manual HTML R Script
Reference Manual PDF


biocViews Clustering, DNASeq, GraphAndNetwork, RNASeq, SingleCell, Software
Version 1.13.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.1.0)
Imports Rcpp (>= 1.0.0), RcppEigen (>=, Matrix, RANN, ape, dendextend, ggplot2, mclust, patchwork, dplyr, grDevices, methods, stats
System Requirements C++11
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Suggests BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
Linking To Rcpp, RcppEigen
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Follow Installation instructions to use this package in your R session.

Source Package HGC_1.13.0.tar.gz
Windows Binary
macOS Binary (x86_64) HGC_1.13.0.tgz
macOS Binary (arm64) HGC_1.13.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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