DOI: 10.18129/B9.bioc.HGC  

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

A fast hierarchical graph-based clustering method

Bioconductor version: Development (3.19)

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 https://github.com/XuegongLab/HGC/tree/HGC4oldRVersion to get HGC package built for R 3.6.

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

Maintainer: XGlab <xglab at mail.tsinghua.edu.cn>

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:



HTML R Script HGC package manual
PDF   Reference Manual
Text   NEWS


biocViews Clustering, DNASeq, GraphAndNetwork, RNASeq, SingleCell, Software
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (2.5 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
LinkingTo Rcpp, RcppEigen
Suggests BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
SystemRequirements C++11
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HGC_1.11.0.tar.gz
Windows Binary HGC_1.11.0.zip
macOS Binary (x86_64) HGC_1.11.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HGC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HGC
Bioc Package Browser https://code.bioconductor.org/browse/HGC/
Package Short Url https://bioconductor.org/packages/HGC/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: