Introduction | Installation | Quick Start | Input data | Run HGC | Run HGC with existing scRNA-seq data processing pipelines | Seurat pipeline | scran pipeline | Visualization | Evaluation of the clustering results | Time complexity analysis of HGC
Package: HGC 1.21.0
XGlab
HGC: A fast hierarchical graph-based clustering method
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.
Authors:
HGC_1.21.0.tar.gz
HGC_1.21.0.zip(r-4.7)HGC_1.21.0.zip(r-4.6)HGC_1.21.0.zip(r-4.5)
HGC_1.21.0.tgz(r-4.6-x86_64)HGC_1.21.0.tgz(r-4.6-arm64)HGC_1.21.0.tgz(r-4.5-x86_64)HGC_1.21.0.tgz(r-4.5-arm64)
HGC_1.21.0.tar.gz(r-4.7-arm64)HGC_1.21.0.tar.gz(r-4.7-x86_64)HGC_1.21.0.tar.gz(r-4.6-arm64)HGC_1.21.0.tar.gz(r-4.6-x86_64)
HGC_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HGC/json (API)
| # Install 'HGC' in R: |
| install.packages('HGC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- Pollen - Embeddings of the Pollen datasets in the principal component space.
On BioConductor:HGC-1.21.0(bioc 3.24)HGC-1.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
singlecellsoftwareclusteringrnaseqgraphandnetworkdnaseqcpp
Last updated from:3930fed132. Checks:12 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 207 | ||
| linux-devel-arm64 | WARNING | 254 | ||
| linux-devel-x86_64 | WARNING | 312 | ||
| source / vignettes | OK | 245 | ||
| linux-release-arm64 | WARNING | 255 | ||
| linux-release-x86_64 | WARNING | 374 | ||
| macos-release-arm64 | WARNING | 189 | ||
| macos-release-x86_64 | WARNING | 469 | ||
| macos-oldrel-arm64 | WARNING | 220 | ||
| macos-oldrel-x86_64 | WARNING | 497 | ||
| windows-devel | WARNING | 230 | ||
| windows-release | WARNING | 270 | ||
| windows-oldrel | WARNING | 237 | ||
| wasm-release | OK | 134 |
Exports:CKNN.ConstructionFindClusteringTreeHGC.dendrogramHGC.parameterHGC.PlotARIsHGC.PlotDendrogramHGC.PlotParameterKNN.ConstructionMST.ConstructionPMST.ConstructionRNN.ConstructionSNN.Construction
Dependencies:apeclicpp11dendextenddigestdplyrfarvergenericsggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMatrixmclustnlmepatchworkpillarpkgconfigR6RANNRColorBrewerRcppRcppEigenrlangS7scalestibbletidyselectutf8vctrsviridisviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Building Unweighted Continuous K Nearest Neighbor Graph | CKNN.Construction |
| The HGC algorithm embedded in Seurat pipeline | FindClusteringTree |
| Hierarchical Graph-based Clustering | HGC.dendrogram |
| Recording the Parameters of the Graph-based Hierarchical Clustering | HGC.parameter |
| Calculating and Visualizing ARIs of the clustering results with given labels | HGC.PlotARIs |
| Visualizing the dendrogram | HGC.PlotDendrogram |
| Visualizing the Parameter Records during Clustering | HGC.PlotParameter |
| Building Unweighted K Nearest Neighbor Graph | KNN.Construction |
| Building Unweighted Minimum Spanning Tree Graph | MST.Construction |
| Building Unweighted Perturbed Minimum Spanning Tree Graph | PMST.Construction |
| Embeddings of the Pollen datasets in the principal component space. | Pollen |
| Building Unweighted epsilon Nearest Neighbor Graph | RNN.Construction |
| Building Unweighted Shared Nearest Neighbor Graph | SNN.Construction |