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A fast hierarchical graph-based clustering method

Bioconductor version: Release (3.19)

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))


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 1.12.0
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_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64) HGC_1.12.0.tgz
macOS Binary (arm64) HGC_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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