├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── CellFunTopic.Rproj ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── Colors.R ├── Plots.R ├── QualityControl.R ├── RunGSEA.R ├── RunSeurat.R ├── data.R ├── readData.R ├── topicModel_predict.R ├── topicModel_utils.R ├── utilities.R └── visualize_in_shiny.R ├── README.md ├── _pkgdown.yml ├── data ├── GO2level.rda ├── HCL_ldaOut.rda ├── MCA_ldaOut.rda ├── MTGENE.rda ├── txid_gene_MT.rda └── txid_species_gene_MT.rda ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── articles │ ├── CellFunTopic.html │ ├── CellFunTopic_files │ │ └── header-attrs-2.14 │ │ │ └── header-attrs.js │ ├── images │ │ ├── shinyappExample.gif │ │ └── workflow.jpg │ ├── index.html │ ├── pre-processing.html │ ├── pre-processing_files │ │ └── header-attrs-2.14 │ │ │ └── header-attrs.js │ ├── shiny_app.html │ ├── shiny_app_files │ │ └── header-attrs-2.14 │ │ │ └── header-attrs.js │ ├── topicmodel_visualization.html │ ├── topicmodel_visualization_files │ │ ├── d3-4.5.0 │ │ │ ├── LICENSE │ │ │ └── d3.min.js │ │ ├── echarts-gl-1.1.2 │ │ │ ├── custom │ │ │ │ ├── renderers.js │ │ │ │ └── style.css │ │ │ ├── dataTool.min.js │ │ │ ├── ecStat.min.js │ │ │ ├── echarts-en.min.js │ │ │ ├── echarts-gl.min.js │ │ │ ├── plugins │ │ │ │ ├── echarts-graph-modularity.min.js │ │ │ │ ├── echarts-leaflet.js │ │ │ │ ├── echarts-liquidfill.min.js │ │ │ │ └── echarts-wordcloud.min.js │ │ │ ├── themes │ │ │ │ ├── auritus.js │ │ │ │ ├── azul.js │ │ │ │ ├── bee-inspired.js │ │ │ │ ├── blue.js │ │ │ │ ├── caravan.js │ │ │ │ ├── carp.js │ │ │ │ ├── chalk.js │ │ │ │ ├── cool.js │ │ │ │ ├── dark-blue.js │ │ │ │ ├── dark-bold.js │ │ │ │ ├── dark-digerati.js │ │ │ │ ├── dark-fresh-cut.js │ │ │ │ ├── dark-mushroom.js │ │ │ │ ├── dark.js │ │ │ │ ├── eduardo.js │ │ │ │ ├── essos.js │ │ │ │ ├── forest.js │ │ │ │ ├── fresh-cut.js │ │ │ │ ├── fruit.js │ │ │ │ ├── gray.js │ │ │ │ ├── green.js │ │ │ │ ├── halloween.js │ │ │ │ ├── helianthus.js │ │ │ │ ├── infographic.js │ │ │ │ ├── inspired.js │ │ │ │ ├── jazz.js │ │ │ │ ├── london.js │ │ │ │ ├── macarons.js │ │ │ │ ├── macarons2.js │ │ │ │ ├── mint.js │ │ │ │ ├── purple-passion.js │ │ │ │ ├── red-velvet.js │ │ │ │ ├── red.js │ │ │ │ ├── roma.js │ │ │ │ ├── royal.js │ │ │ │ ├── sakura.js │ │ │ │ ├── shine.js │ │ │ │ ├── tech-blue.js │ │ │ │ ├── vintage.js │ │ │ │ ├── walden.js │ │ │ │ ├── wef.js │ │ │ │ ├── weforum.js │ │ │ │ ├── westeros.js │ │ │ │ └── wonderland.js │ │ │ └── world.js │ │ ├── echarts-graph-modularity-1.1.0 │ │ │ ├── echarts-graph-modularity.min.js │ │ │ ├── echarts-leaflet.js │ │ │ ├── echarts-liquidfill.min.js │ │ │ └── echarts-wordcloud.min.js │ │ ├── echarts4r-4.8.0 │ │ │ ├── custom │ │ │ │ ├── renderers.js │ │ │ │ └── style.css │ │ │ ├── dataTool.min.js │ │ │ ├── ecStat.min.js │ │ │ ├── echarts-en.min.js │ │ │ ├── echarts-gl.min.js │ │ │ ├── i18n │ │ │ │ ├── langCS-obj.js │ │ │ │ ├── langCS.js │ │ │ │ ├── langDE-obj.js │ │ │ │ ├── langDE.js │ │ │ │ ├── langEN-obj.js │ │ │ │ ├── langEN.js │ │ │ │ ├── langES-obj.js │ │ │ │ ├── langES.js │ │ │ │ ├── langFI-obj.js │ │ │ │ ├── langFI.js │ │ │ │ ├── langFR-obj.js │ │ │ │ ├── langFR.js │ │ │ │ ├── langJA-obj.js │ │ │ │ ├── langJA.js │ │ │ │ ├── langPL-obj.js │ │ │ │ ├── langPL.js │ │ │ │ ├── langPT-br-obj.js │ │ │ │ ├── langPT-br.js │ │ │ │ ├── langRU-obj.js │ │ │ │ ├── langRU.js │ │ │ │ ├── langSI-obj.js │ │ │ │ ├── langSI.js │ │ │ │ ├── langTH-obj.js │ │ │ │ ├── langTH.js │ │ │ │ ├── langZH-obj.js │ │ │ │ └── langZH.js │ │ │ ├── plugins │ │ │ │ ├── echarts-graph-modularity.min.js │ │ │ │ ├── echarts-leaflet.js │ │ │ │ ├── echarts-liquidfill.min.js │ │ │ │ └── echarts-wordcloud.min.js │ │ │ ├── themes │ │ │ │ ├── auritus.js │ │ │ │ ├── azul.js │ │ │ │ ├── bee-inspired.js │ │ │ │ ├── blue.js │ │ │ │ ├── caravan.js │ │ │ │ ├── carp.js │ │ │ │ ├── chalk.js │ │ │ │ ├── cool.js │ │ │ │ ├── dark-blue.js │ │ │ │ ├── dark-bold.js │ │ │ │ ├── dark-digerati.js │ │ │ │ ├── dark-fresh-cut.js │ │ │ │ ├── dark-mushroom.js │ │ │ │ ├── dark.js │ │ │ │ ├── eduardo.js │ │ │ │ ├── essos.js │ │ │ │ ├── forest.js │ │ │ │ ├── fresh-cut.js │ │ │ │ ├── fruit.js │ │ │ │ ├── gray.js │ │ │ │ ├── green.js │ │ │ │ ├── halloween.js │ │ │ │ ├── helianthus.js │ │ │ │ ├── infographic.js │ │ │ │ ├── inspired.js │ │ │ │ ├── jazz.js │ │ │ │ ├── london.js │ │ │ │ ├── macarons.js │ │ │ │ ├── macarons2.js │ │ │ │ ├── mint.js │ │ │ │ ├── purple-passion.js │ │ │ │ ├── red-velvet.js │ │ │ │ ├── red.js │ │ │ │ ├── roma.js │ │ │ │ ├── royal.js │ │ │ │ ├── sakura.js │ │ │ │ ├── shine.js │ │ │ │ ├── tech-blue.js │ │ │ │ ├── vintage.js │ │ │ │ ├── walden.js │ │ │ │ ├── wef.js │ │ │ │ ├── weforum.js │ │ │ │ ├── westeros.js │ │ │ │ └── wonderland.js │ │ │ └── world.js │ │ ├── echarts4r-binding-0.3.3 │ │ │ └── echarts4r.js │ │ ├── echarts4r-binding-0.4.4 │ │ │ └── echarts4r.js │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-8-1.png │ │ ├── header-attrs-2.14 │ │ │ └── header-attrs.js │ │ ├── htmlwidgets-1.5.2 │ │ │ └── htmlwidgets.js │ │ ├── htmlwidgets-1.5.3 │ │ │ └── htmlwidgets.js │ │ ├── sankey-1 │ │ │ ├── d3-4.5.0 │ │ │ │ ├── LICENSE │ │ │ │ └── d3.min.js │ │ │ └── sankey.js │ │ ├── sankeyNetwork-binding-0.4 │ │ │ └── sankeyNetwork.js │ │ ├── wordcloud2-0.0.1 │ │ │ ├── hover.js │ │ │ ├── wordcloud.css │ │ │ └── wordcloud2-all.js │ │ └── wordcloud2-binding-0.2.1 │ │ │ └── wordcloud2.js │ ├── transfer_annotation.html │ ├── transfer_annotation_files │ │ └── header-attrs-2.14 │ │ │ └── header-attrs.js │ ├── transfer_topicmodel.html │ ├── transfer_topicmodel_files │ │ ├── d3-4.5.0 │ │ │ ├── LICENSE │ │ │ └── d3.min.js │ │ ├── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ └── unnamed-chunk-16-1.png │ │ ├── header-attrs-2.14 │ │ │ └── header-attrs.js │ │ ├── htmlwidgets-1.5.2 │ │ │ └── htmlwidgets.js │ │ ├── sankey-1 │ │ │ ├── d3-4.5.0 │ │ │ │ ├── LICENSE │ │ │ │ └── d3.min.js │ │ │ └── sankey.js │ │ └── sankeyNetwork-binding-0.4 │ │ │ └── sankeyNetwork.js │ ├── visualization_gsea.html │ └── visualization_gsea_files │ │ ├── figure-html │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-12-1.png │ │ ├── unnamed-chunk-13-1.png │ │ ├── unnamed-chunk-14-1.png │ │ ├── unnamed-chunk-15-1.png │ │ ├── unnamed-chunk-16-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-5-1.png │ │ ├── unnamed-chunk-6-1.png │ │ ├── unnamed-chunk-7-1.png │ │ ├── unnamed-chunk-8-1.png │ │ └── unnamed-chunk-9-1.png │ │ └── header-attrs-2.14 │ │ └── header-attrs.js ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── CalMTpercent.html │ ├── Cosine_networkByGSEA.html │ ├── DetectGeneIDtype.html │ ├── GO2level.html │ ├── GOboxplot.html │ ├── GOcircleplot.html │ ├── HCL_ldaOut.html │ ├── ID2Description.html │ ├── MCA_ldaOut.html │ ├── MTGENE.html │ ├── QCfun.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── RunGSEA.html │ ├── RunSeurat.html │ ├── Topterms_Topic.html │ ├── circleplot.html │ ├── cluster_topic_hmp.html │ ├── clustercorplot.html │ ├── cosine_heatmap2.html │ ├── cosine_hive.html │ ├── cosine_network_cluster.html │ ├── cosine_network_cluster2.html │ ├── cosine_network_term.html │ ├── cosineheatmap.html │ ├── cosinehmp_cluster.html │ ├── edge_bundling_GSEA.html │ ├── embeddedplot.html │ ├── gseaHeatmap.html │ ├── hierarchyplot_tree.html │ ├── hist_cluster_topic.html │ ├── hist_topic_term.html │ ├── index.html │ ├── lda.rep.html │ ├── oversample_ref.html │ ├── pathwayScatterplot.html │ ├── pathway_unique_shared.html │ ├── plot_sankey.html │ ├── plotindex.html │ ├── predictFun.html │ ├── readData.html │ ├── runLDA.html │ ├── sankey_comparison.html │ ├── scPalette-1.png │ ├── scPalette.html │ ├── scPalette2-1.png │ ├── scPalette2-2.png │ ├── scPalette2.html │ ├── scPalette3-1.png │ ├── scPalette3.html │ ├── simplifyEnrichmentplot.html │ ├── topicNW1.html │ ├── topicNW2.html │ ├── topicNW3.html │ ├── topicProb.html │ ├── transfer_LDA.html │ ├── txid_gene_MT.html │ ├── txid_species_gene_MT.html │ ├── umap_cluster.html │ ├── visualize_in_shiny.html │ └── wordcloud_topic.html ├── inst └── shiny │ ├── Utils │ ├── Colors.R │ ├── Developer.server.R │ └── UI_functions.R │ ├── focus │ ├── focus.server.R │ └── focus.ui.R │ ├── global.R │ ├── overview │ ├── overview.plot.R │ ├── overview.server.R │ └── overview.ui.R │ ├── server.R │ ├── topicModel │ ├── topicModel.server.R │ └── topicModel.ui.R │ ├── ui.R │ └── www │ ├── custom.css │ └── profile.png ├── man ├── CalMTpercent.Rd ├── Cosine_networkByGSEA.Rd ├── DetectGeneIDtype.Rd ├── GO2level.Rd ├── GOboxplot.Rd ├── GOcircleplot.Rd ├── HCL_ldaOut.Rd ├── ID2Description.Rd ├── MCA_ldaOut.Rd ├── MTGENE.Rd ├── QCfun.Rd ├── RunGSEA.Rd ├── RunSeurat.Rd ├── Topterms_Topic.Rd ├── circleplot.Rd ├── cluster_topic_hmp.Rd ├── clustercorplot.Rd ├── cosine_heatmap2.Rd ├── cosine_hive.Rd ├── cosine_network_cluster.Rd ├── cosine_network_cluster2.Rd ├── cosine_network_term.Rd ├── cosineheatmap.Rd ├── cosinehmp_cluster.Rd ├── edge_bundling_GSEA.Rd ├── embeddedplot.Rd ├── gseaHeatmap.Rd ├── hierarchyplot_tree.Rd ├── hist_cluster_topic.Rd ├── hist_topic_term.Rd ├── lda.rep.Rd ├── oversample_ref.Rd ├── pathwayScatterplot.Rd ├── pathway_unique_shared.Rd ├── plot_sankey.Rd ├── plotindex.Rd ├── predictFun.Rd ├── readData.Rd ├── runLDA.Rd ├── sankey_comparison.Rd ├── scPalette.Rd ├── scPalette2.Rd ├── scPalette3.Rd ├── simplifyEnrichmentplot.Rd ├── 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