Files in dputhier/scigenex
The scigenex package (Single-Cell Informative GENe Explorer)

.Rbuildignore
.github/.gitignore
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
Makefile
NAMESPACE
NEWS.md R/ClusterSet_class.R R/Visium_hull.R R/cluster_stats.R R/clusterset_report.R R/compare_gene_sets.R R/convert.R R/dataset_doc.R R/dist2border.R R/enrichment_analysis.R R/filter_gene_clusters.R R/gene_clustering.R R/get_data_for_scigenex.R R/get_genes.R R/import_package.R R/module_quality_scores.R R/plot_profiles.R R/plot_spatial.R R/reorder_genes.R R/select_genes.R R/top_by_go.R R/top_genes.R R/utils.R R/visualization.R R/zzz.R README.Rmd README.md
_pkgdown.yml
changelog.md
codecov.yml
data/complex9.rda
data/complex9Noisy.rda
data/lymph_node_selected_spot.rda
data/lymph_node_selected_spot_2.rda
docs/404.html
docs/articles/index.html
docs/articles/scigenex.html
docs/articles/usage.html
docs/articles/usage_files/figure-html/classicalsteps-1.png
docs/articles/usage_files/figure-html/heatspatial-1.png
docs/articles/usage_files/figure-html/hull_white-1.png
docs/articles/usage_files/figure-html/plot_spatial-1.png
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docs/articles/usage_files/figure-html/seurat_classes-1.png
docs/articles/usage_files/figure-html/topoclusters-1.png
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docs/articles/usage_files/htmlwidgets-1.6.2/htmlwidgets.js
docs/articles/usage_files/iheatmapr-binding-0.5.1/iheatmapr.js
docs/articles/usage_files/plotlyjs-1.27.1/LICENSE.txt
docs/articles/usage_files/plotlyjs-1.27.1/plotly-htmlwidgets.css
docs/articles/usage_files/plotlyjs-1.27.1/plotly-latest.min.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/changelog.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ClusterSet-class-1.png
docs/reference/ClusterSet-class.html
docs/reference/Rplot001.png
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docs/reference/check_format_cluster_set.html
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docs/reference/clust_size-ClusterSet-method.html
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docs/reference/cluster_set_from_matrix-1.png
docs/reference/cluster_set_from_matrix.html
docs/reference/cluster_set_from_seurat-1.png
docs/reference/cluster_set_from_seurat.html
docs/reference/cluster_set_report.html
docs/reference/cluster_set_to_xls-ClusterSet-method.html
docs/reference/cluster_set_to_xls.html
docs/reference/cluster_stats-ClusterSet-method.html
docs/reference/cluster_stats.html
docs/reference/col_names-ClusterSet-method.html
docs/reference/col_names.html
docs/reference/colors_for_gradient.html
docs/reference/compare_genesets.html
docs/reference/complex9.html
docs/reference/complex9Noisy.html
docs/reference/construct_new_graph.html
docs/reference/create_3_rnd_clust.html
docs/reference/create_4_rnd_clust.html
docs/reference/create_rand_str.html
docs/reference/dim-ClusterSet-method.html
docs/reference/discrete_palette.html
docs/reference/display_hull-1.png
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docs/reference/display_hull-3.png
docs/reference/display_hull.html
docs/reference/enrich_go-ClusterSet-method.html
docs/reference/enrich_go.html
docs/reference/filter_by_dot_prod.html
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docs/reference/filter_cluster_sd.html
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docs/reference/filter_nb_supporting_cells.html
docs/reference/gene_cluster-ClusterSet-method.html
docs/reference/gene_cluster.html
docs/reference/gene_clustering.html
docs/reference/getFlippedTissueCoordinates.html
docs/reference/get_data_for_scigenex.html
docs/reference/get_genes.html
docs/reference/get_verbosity.html
docs/reference/grapes-in-grapes-character-ClusterSet-method.html
docs/reference/grep_clust-ClusterSet-method.html
docs/reference/grep_clust.html
docs/reference/index.html
docs/reference/install_mcl.html
docs/reference/keep_dbf_graph.html
docs/reference/load_example_dataset.html
docs/reference/lymph_node_selected_spot.html
docs/reference/lymph_node_selected_spot_2.html
docs/reference/mcl_system_cmd.html
docs/reference/module_quality_scores-ClusterSet-method.html
docs/reference/module_quality_scores.html
docs/reference/nclust-ClusterSet-method.html
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docs/reference/ncol.ClusterSet.html
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docs/reference/plot_cluster_stats.html
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docs/reference/plot_cmp_genesets.html
docs/reference/plot_dist-1.png
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docs/reference/plot_ggheatmap-1.png
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docs/reference/plot_ggheatmap-ClusterSet-method.html
docs/reference/plot_ggheatmap.html
docs/reference/plot_heatmap-1.png
docs/reference/plot_heatmap.html
docs/reference/plot_markers_to_clusters-1.png
docs/reference/plot_markers_to_clusters-ClusterSet-method-1.png
docs/reference/plot_markers_to_clusters-ClusterSet-method.html
docs/reference/plot_markers_to_clusters.html
docs/reference/plot_profiles-1.png
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docs/reference/plot_profiles-3.png
docs/reference/plot_profiles.html
docs/reference/plot_spatial-1.png
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docs/reference/plot_spatial_panel-1.png
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docs/reference/plot_spatial_panel.html
docs/reference/plot_stratum-1.png
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docs/reference/plot_stratum.html
docs/reference/print_msg.html
docs/reference/print_stat.html
docs/reference/rename_clust-ClusterSet-method.html
docs/reference/rename_clust.html
docs/reference/reorder_clust-ClusterSet-method.html
docs/reference/reorder_clust.html
docs/reference/reorder_genes-ClusterSet-method.html
docs/reference/reorder_genes.html
docs/reference/row_names-ClusterSet-method.html
docs/reference/row_names.html
docs/reference/select_genes.html
docs/reference/set_verbosity.html
docs/reference/show-ClusterSet-method.html
docs/reference/show_methods.html
docs/reference/stratify_seurat-1.png
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docs/reference/stratify_seurat.html
docs/reference/sub-ClusterSet-ANY-ANY-ANY-method.html
docs/reference/top_by_go-ClusterSet-method.html
docs/reference/top_by_go.html
docs/reference/top_genes-ClusterSet-method.html
docs/reference/top_genes.html
docs/reference/viz_enrich-ClusterSet-method-1.png
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docs/reference/viz_enrich-ClusterSet-method.html
docs/reference/viz_enrich.html
docs/reference/which_clust-ClusterSet-method.html
docs/reference/which_clust.html
docs/sitemap.xml
inst/sticker/scigenex_logo.png
man/ClusterSet-class.Rd man/check_format_cluster_set.Rd man/clust_names-ClusterSet-method.Rd man/clust_names.Rd man/clust_size-ClusterSet-method.Rd man/clust_size.Rd man/cluster_set_from_matrix.Rd man/cluster_set_from_seurat.Rd man/cluster_set_report.Rd man/cluster_set_to_xls-ClusterSet-method.Rd man/cluster_set_to_xls.Rd man/cluster_stats-ClusterSet-method.Rd man/cluster_stats.Rd man/col_names-ClusterSet-method.Rd man/col_names.Rd man/colors_for_gradient.Rd man/compare_genesets.Rd man/complex9.Rd man/complex9Noisy.Rd man/construct_new_graph.Rd man/create_3_rnd_clust.Rd man/create_4_rnd_clust.Rd man/create_rand_str.Rd man/dim-ClusterSet-method.Rd man/discrete_palette.Rd man/display_hull.Rd man/enrich_go-ClusterSet-method.Rd man/enrich_go.Rd man/filter_by_dot_prod.Rd man/filter_cluster_sd.Rd man/filter_cluster_size.Rd man/filter_nb_supporting_cells.Rd man/gene_cluster-ClusterSet-method.Rd man/gene_cluster.Rd man/gene_clustering.Rd man/getFlippedTissueCoordinates.Rd man/get_data_for_scigenex.Rd man/get_genes.Rd man/get_verbosity.Rd man/grapes-in-grapes-character-ClusterSet-method.Rd man/grep_clust-ClusterSet-method.Rd man/grep_clust.Rd man/install_mcl.Rd man/keep_dbf_graph.Rd man/load_example_dataset.Rd man/lymph_node_selected_spot.Rd man/lymph_node_selected_spot_2.Rd man/mcl_system_cmd.Rd man/module_quality_scores-ClusterSet-method.Rd man/module_quality_scores.Rd man/nclust-ClusterSet-method.Rd man/nclust.Rd man/ncol.ClusterSet.Rd man/nrow.ClusterSet.Rd man/plot_clust_enrichments-ClusterSet-method.Rd man/plot_clust_enrichments.Rd man/plot_cluster_stats.Rd man/plot_cmp_genesets.Rd man/plot_dist.Rd man/plot_ggheatmap-ClusterSet-method.Rd man/plot_ggheatmap.Rd man/plot_heatmap.Rd man/plot_markers_to_clusters-ClusterSet-method.Rd man/plot_markers_to_clusters.Rd man/plot_profiles.Rd man/plot_spatial.Rd man/plot_spatial_panel.Rd man/plot_stratum.Rd man/print_msg.Rd man/print_stat.Rd man/rename_clust-ClusterSet-method.Rd man/rename_clust.Rd man/reorder_clust-ClusterSet-method.Rd man/reorder_clust.Rd man/reorder_genes-ClusterSet-method.Rd man/reorder_genes.Rd man/row_names-ClusterSet-method.Rd man/row_names.Rd man/select_genes.Rd man/set_verbosity.Rd man/show-ClusterSet-method.Rd man/show_methods.Rd man/stratify_seurat.Rd man/sub-ClusterSet-ANY-ANY-ANY-method.Rd man/top_by_go-ClusterSet-method.Rd man/top_by_go.Rd man/top_genes-ClusterSet-method.Rd man/top_genes.Rd man/viz_enrich-ClusterSet-method.Rd man/viz_enrich.Rd man/which_clust-ClusterSet-method.Rd man/which_clust.Rd tests/testthat.R tests/testthat/test.ClusterSet_class.R tests/testthat/test.Visium_hull.R tests/testthat/test.cluster_stats.R tests/testthat/test.compare_gene_sets.R tests/testthat/test.convert.R
tests/testthat/test.dataset_doc.R
tests/testthat/test.dist2border.R tests/testthat/test.enrichment_analysis.R tests/testthat/test.filter_gene_clusters.R tests/testthat/test.gene_clustering.R tests/testthat/test.get_data_for_scigenex.R tests/testthat/test.get_genes.R tests/testthat/test.plot_profiles.R tests/testthat/test.plot_spatial.R tests/testthat/test.reorder_genes.R tests/testthat/test.select_genes.R tests/testthat/test.top_by_go.R tests/testthat/test.top_genes.R tests/testthat/test.utils.R tests/testthat/test.visualization.R vignettes/usage.Rmd
dputhier/scigenex documentation built on Jan. 29, 2024, 3:40 p.m.