1. Load the package | 2. Example Data set | 3. Pre-processing the data | 4. Determine the tuning parameter | 5. Run ClussCluster | Viewing Clustering Results | Cell-type-specific signature genes | 6. Plot | 7. References
Package: ClussCluster 0.1.0
ClussCluster: Simultaneous Detection of Clusters and Cluster-Specific Genes in High-Throughput Transcriptome Data
Implements a new method 'ClussCluster' descried in Ge Jiang and Jun Li, "Simultaneous Detection of Clusters and Cluster-Specific Genes in High-throughput Transcriptome Data" (Unpublished). Simultaneously perform clustering analysis and signature gene selection on high-dimensional transcriptome data sets. To do so, 'ClussCluster' incorporates a Lasso-type regularization penalty term to the objective function of K- means so that cell-type-specific signature genes can be identified while clustering the cells.
Authors:
ClussCluster_0.1.0.tar.gz
ClussCluster_0.1.0.zip(r-4.7-any)ClussCluster_0.1.0.zip(r-4.6-any)ClussCluster_0.1.0.zip(r-4.5-any)
ClussCluster_0.1.0.tgz(r-4.6-any)ClussCluster_0.1.0.tgz(r-4.5-any)
ClussCluster_0.1.0.tar.gz(r-4.7-any)ClussCluster_0.1.0.tar.gz(r-4.6-any)
ClussCluster_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ClussCluster/json (API)
| # Install 'ClussCluster' in R: |
| install.packages('ClussCluster', repos = c('https://jli-stat.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:ac393fec37. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 139 | ||
| source / vignettes | OK | 155 | ||
| linux-release-x86_64 | NOTE | 144 | ||
| macos-release-arm64 | NOTE | 102 | ||
| macos-oldrel-arm64 | NOTE | 118 | ||
| windows-devel | NOTE | 84 | ||
| windows-release | NOTE | 94 | ||
| windows-oldrel | NOTE | 71 | ||
| wasm-release | OK | 153 |
Exports:ClussClusterClussCluster_Gapfilter_geneplot_ClussClusterplot_ClussCluster_Gapprint_ClussClusterprint_ClussCluster_Gaptop.m.hm
Dependencies:clicpp11farverformatRfutile.loggerfutile.optionsggplot2gluegtableisobandlabelinglambda.rlifecyclemagrittrplyrR6RColorBrewerRcppreshape2rlangS7scalesstringistringrvctrsVennDiagramviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Performs simultaneous detection of cell types and cell-type-specific signature genes | ClussCluster ClussCluster_Gap |
| Gene Filter | filter_gene |
| A truncated subset of the scRNA-seq expression data set from Hou et.al (2016) | Hou_sim |
| Plots the results of 'ClussCluster' | plot_ClussCluster top.m.hm |
| Plots the results of 'ClussCluster_Gap' | plot_ClussCluster_Gap |
| Prints out the results of 'ClussCluster' | print_ClussCluster |
| Prints out the results of 'ClussCluster_Gap' Prints the gap statistics and number of genes selected for each candidate tuning parameter. | print_ClussCluster_Gap |
| A simulated expression data set. | sim_dat |
