HGC

DOI: 10.18129/B9.bioc.HGC    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see HGC.

A fast hierarchical graph-based clustering method

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

HTML	R Script	HGC package manual
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DNASeq, GraphAndNetwork, RNASeq, SingleCell, Software
Version	1.0.3
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
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
LinkingTo	Rcpp, RcppEigen
Suggests	BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
SystemRequirements	C++11
Enhances
URL
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_1.0.3.tar.gz
Windows Binary	HGC_1.0.3.zip
macOS 10.13 (High Sierra)	HGC_1.0.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HGC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HGC
Package Short Url	https://bioconductor.org/packages/HGC/
Package Downloads Report	Download Stats