Package: ClusterGVis 1.0.0

Jun Zhang

ClusterGVis: One-Step to Cluster and Visualize Gene Expression Data

Provides a streamlined workflow for clustering and visualizing gene expression patterns, particularly from time-series RNA-Seq and single-cell experiments. The package is designed to integrate seamlessly within the Bioconductor ecosystem by operating directly on standard data classes such as `SummarizedExperiment` and `SingleCellExperiment`. It implements common clustering algorithms (e.g., k-means, fuzzy c-means) and generates a suite of publication-ready visualizations to explore co-expressed gene modules. Functions are also included to facilitate the visualization of clustering results derived from other popular tools.

Authors:Jun Zhang [aut, cre, cph]

ClusterGVis_1.0.0.tar.gz
ClusterGVis_1.0.0.zip(r-4.7)ClusterGVis_1.0.0.zip(r-4.6)ClusterGVis_1.0.0.zip(r-4.5)
ClusterGVis_1.0.0.tgz(r-4.6-any)ClusterGVis_1.0.0.tgz(r-4.5-any)
ClusterGVis_1.0.0.tar.gz(r-4.7-any)ClusterGVis_1.0.0.tar.gz(r-4.6-any)
ClusterGVis_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
ClusterGVis/json (API)
NEWS

# Install 'ClusterGVis' in R:
install.packages('ClusterGVis', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/junjunlab/clustergvis/issues

Datasets:
  • BEAM_res - This is a test data for this package
  • exps - This is a test data for this package
  • HSMM - This is a test data for this package
  • net - This is a test data for this package
  • pbmc_subset - This is a test data for this package
  • sig_gene_names - This is a test data for this package
  • termanno - This is a test data for this package
  • termanno2 - This is a test data for this package

On BioConductor:ClusterGVis-1.1.0(bioc 3.24)ClusterGVis-1.0.0(bioc 3.23)

rnaseqtranscriptomicsvisualizationsinglecellgeneexpressionclusteringcomplexheatmapgene-clusteringgene-expressionmfuzz

7.65 score 376 stars 148 downloads 7 exports 151 dependencies

Last updated from:cd557acaa4 (on RELEASE_3_23). Checks:1 NOTE, 2 WARNING, 7 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE300
linux-devel-x86_64WARNING608
source / vignettesOK366
linux-release-x86_64OK601
macos-release-arm64OK380
macos-oldrel-arm64OK372
windows-develWARNING546
windows-releaseOK469
windows-oldrelOK455
wasm-releaseOK274

Exports:clusterDataenrichClustergetClustersplot_genes_branched_heatmap2plot_pseudotime_heatmap2prepareDataFromscRNAvisCluster

Dependencies:abindassortheadbackportsbase64encbeachmatBHBiobaseBiocGenericsBiocParallelbootbroombslibcachemcarcarDataclasscliclustercodetoolscolorRampscolorspacecorrplotcowplotcpp11crosstalkDelayedArraydendextendDerivdigestdoBydplyrDTe1071ellipseemmeansestimabilityevaluatefactoextraFactoMineRfarverfastmapflashClustfontawesomeforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetsigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivotelpbkrtestpillarpkgconfigplyrpolynompromisesproxypurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrmarkdownrstatixS4ArraysS4VectorsS7sassscalesscatterplot3dscuttleSeqinfoSingleCellExperimentsnowSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDatetinytexurcautf8vctrsVGAMviridisviridisLitewithrxfunXVectoryamlzoo

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Last update: 2025-11-13
Started: 2025-06-16