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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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HGC")

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

Documentation

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

browseVignettes("HGC")
HGC package manual HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, DNASeq, GraphAndNetwork, RNASeq, SingleCell, Software
Version 1.11.0
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 (>= 0.3.2.0), Matrix, RANN, ape, dendextend, ggplot2, mclust, patchwork, dplyr, grDevices, methods, stats
System Requirements C++11
URL
See More
Suggests BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
Linking To Rcpp, RcppEigen
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report 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) HGC_1.11.0.tgz
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