Package: ClussCluster 0.1.0
Li Jun
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and Jun Li, "Simultaneous Detection of Clusters and Cluster-Specific Genes in High-throughput Transcriptome Data" (Unpublished).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.tar.gz(r-4.5-noble)ClussCluster_0.1.0.tar.gz(r-4.4-noble)
ClussCluster_0.1.0.tgz(r-4.4-emscripten)ClussCluster_0.1.0.tgz(r-4.3-emscripten)
ClussCluster.pdf |ClussCluster.html✨
ClussCluster/json (API)
| # Install 'ClussCluster' in R: |
| install.packages('ClussCluster', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:ac393fec37. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 08 2024 |
| R-4.5-linux | NOTE | Dec 08 2024 |
Exports:ClussClusterClussCluster_Gapfilter_geneplot_ClussClusterplot_ClussCluster_Gapprint_ClussClusterprint_ClussCluster_Gaptop.m.hm
Dependencies:clicolorspacefansifarverformatRfutile.loggerfutile.optionsggplot2gluegtableisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsVennDiagramviridisLitewithr
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 |