HGC
This is the development version of HGC; for the stable release version, see HGC.
A fast hierarchical graph-based clustering method
DOI: 10.18129/B9.bioc.HGC
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, DNASeq, GraphAndNetwork, RNASeq, SingleCell, Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 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_1.21.0.tar.gz |
| Windows Binary (x86_64) | HGC_1.21.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | HGC_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | HGC_1.21.0.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 |