HGC
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see HGC.
A fast hierarchical graph-based clustering method
Bioconductor version: 3.14
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("HGC")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("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")| HGC package manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DNASeq, GraphAndNetwork, RNASeq, SingleCell, Software |
| Version | 1.2.0 |
| 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HGC_1.2.0.tar.gz |
| Windows Binary | HGC_1.2.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | HGC_1.2.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |