Package: HGC 1.15.0
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_1.15.0.tar.gz
HGC_1.15.0.zip(r-4.5)HGC_1.15.0.zip(r-4.4)HGC_1.15.0.zip(r-4.3)
HGC_1.15.0.tgz(r-4.4-x86_64)HGC_1.15.0.tgz(r-4.4-arm64)HGC_1.15.0.tgz(r-4.3-x86_64)HGC_1.15.0.tgz(r-4.3-arm64)
HGC_1.15.0.tar.gz(r-4.5-noble)HGC_1.15.0.tar.gz(r-4.4-noble)
HGC_1.15.0.tgz(r-4.4-emscripten)HGC_1.15.0.tgz(r-4.3-emscripten)
HGC.pdf |HGC.html✨
HGC/json (API)
NEWS
| # Install 'HGC' in R: |
| install.packages('HGC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- Pollen - Embeddings of the Pollen datasets in the principal component space.
On BioConductor:HGC-1.13.0(bioc 3.20)HGC-1.12.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
singlecellsoftwareclusteringrnaseqgraphandnetworkdnaseq
Last updated 23 days agofrom:c8f04e4ee8. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.5-linux-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 30 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 30 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 30 2024 |
Exports:CKNN.ConstructionFindClusteringTreeHGC.dendrogramHGC.parameterHGC.PlotARIsHGC.PlotDendrogramHGC.PlotParameterKNN.ConstructionMST.ConstructionPMST.ConstructionRNN.ConstructionSNN.Construction
Dependencies:apeclicolorspacedendextenddigestdplyrfansifarvergenericsggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmclustmgcvmunsellnlmepatchworkpillarpkgconfigR6RANNRColorBrewerRcppRcppEigenrlangscalestibbletidyselectutf8vctrsviridisviridisLitewithr
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 |