├── .Rbuildignore ├── .Rhistory ├── .gitattributes ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── 1.getClusters.R ├── 2.clusterData.R ├── 3.enrichCluster.R ├── 4.visCluster.R ├── data.R ├── filter.std.R ├── monocleHeatmap.R ├── prepareDataFromscRNA.R └── utils.R ├── README.md ├── data ├── BEAM_res.rda ├── HSMM.rda ├── exps.rda ├── net.rda ├── pbmc_subset.rda ├── sig_gene_names.rda ├── termanno.rda └── termanno2.rda ├── inst └── CITATION ├── man ├── DataSet.Rd ├── cell_data_set-class.Rd ├── clusterData.Rd ├── enrichCluster.Rd ├── exprs-cell_data_set-method.Rd ├── exprs.Rd ├── filter.std-modified-by-Mfuzz-filter.std.Rd ├── getClusters.Rd ├── plot_genes_branched_heatmap2.Rd ├── plot_pseudotime_heatmap2.Rd ├── prepareDataFromscRNA.Rd ├── pseudotime.Rd ├── traverseTree.Rd └── visCluster.Rd ├── tests ├── testthat.R └── testthat │ ├── test-clusterData.R │ ├── test-getClusters.R │ └── test-visCluster.R └── vignettes ├── .gitignore ├── clusterGVis.png ├── clusterGvis_graphic_abstract.jpg └── vignette.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/.Rhistory -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | YEAR: 2025 2 | COPYRIGHT HOLDER: ClusterGVis authors 3 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/LICENSE.md -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- 1 | ## Changes in version 0.99.0 (2025-08-01) 2 | 3 | Submitted to Bioconductor 4 | -------------------------------------------------------------------------------- /R/1.getClusters.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/1.getClusters.R -------------------------------------------------------------------------------- /R/2.clusterData.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/2.clusterData.R -------------------------------------------------------------------------------- /R/3.enrichCluster.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/3.enrichCluster.R -------------------------------------------------------------------------------- /R/4.visCluster.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/4.visCluster.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/data.R -------------------------------------------------------------------------------- /R/filter.std.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/filter.std.R -------------------------------------------------------------------------------- /R/monocleHeatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/monocleHeatmap.R -------------------------------------------------------------------------------- /R/prepareDataFromscRNA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/prepareDataFromscRNA.R -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/R/utils.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/README.md -------------------------------------------------------------------------------- /data/BEAM_res.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/data/BEAM_res.rda -------------------------------------------------------------------------------- /data/HSMM.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/data/HSMM.rda -------------------------------------------------------------------------------- /data/exps.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/data/exps.rda -------------------------------------------------------------------------------- /data/net.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/data/net.rda -------------------------------------------------------------------------------- /data/pbmc_subset.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/data/pbmc_subset.rda -------------------------------------------------------------------------------- /data/sig_gene_names.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/data/sig_gene_names.rda -------------------------------------------------------------------------------- /data/termanno.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/data/termanno.rda -------------------------------------------------------------------------------- /data/termanno2.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/data/termanno2.rda -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/inst/CITATION -------------------------------------------------------------------------------- /man/DataSet.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/DataSet.Rd -------------------------------------------------------------------------------- /man/cell_data_set-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/cell_data_set-class.Rd -------------------------------------------------------------------------------- /man/clusterData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/clusterData.Rd -------------------------------------------------------------------------------- /man/enrichCluster.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/enrichCluster.Rd -------------------------------------------------------------------------------- /man/exprs-cell_data_set-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/exprs-cell_data_set-method.Rd -------------------------------------------------------------------------------- /man/exprs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/exprs.Rd -------------------------------------------------------------------------------- /man/filter.std-modified-by-Mfuzz-filter.std.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/filter.std-modified-by-Mfuzz-filter.std.Rd -------------------------------------------------------------------------------- /man/getClusters.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/getClusters.Rd -------------------------------------------------------------------------------- /man/plot_genes_branched_heatmap2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/plot_genes_branched_heatmap2.Rd -------------------------------------------------------------------------------- /man/plot_pseudotime_heatmap2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/plot_pseudotime_heatmap2.Rd -------------------------------------------------------------------------------- /man/prepareDataFromscRNA.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/prepareDataFromscRNA.Rd -------------------------------------------------------------------------------- /man/pseudotime.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/pseudotime.Rd -------------------------------------------------------------------------------- /man/traverseTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/traverseTree.Rd -------------------------------------------------------------------------------- /man/visCluster.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/man/visCluster.Rd -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test-clusterData.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/tests/testthat/test-clusterData.R -------------------------------------------------------------------------------- /tests/testthat/test-getClusters.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/tests/testthat/test-getClusters.R -------------------------------------------------------------------------------- /tests/testthat/test-visCluster.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/tests/testthat/test-visCluster.R -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | *.R 3 | -------------------------------------------------------------------------------- /vignettes/clusterGVis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/vignettes/clusterGVis.png -------------------------------------------------------------------------------- /vignettes/clusterGvis_graphic_abstract.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/vignettes/clusterGvis_graphic_abstract.jpg -------------------------------------------------------------------------------- /vignettes/vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/junjunlab/ClusterGVis/HEAD/vignettes/vignette.Rmd --------------------------------------------------------------------------------