├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── data.R ├── debug.R ├── haystack.R ├── haystack_IO.R ├── haystack_clustering.R ├── haystack_clustering_highD.R ├── haystack_continuous.R ├── haystack_highD.R ├── haystack_visualization.R ├── randomization.R ├── s3.R ├── singleCellHaystack-package.R └── sparse.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── data-raw ├── .gitignore ├── icon.csv ├── process_vignette.R ├── source_moca_100k.Rmd ├── source_pseudotime.Rmd └── toy_data.R ├── data └── toy.rda ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── articles │ ├── a01_toy_example.html │ ├── a01_toy_example_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-6-1.png │ ├── examples │ │ ├── a02_example_scRNAseq.html │ │ ├── a02_example_scRNAseq_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-10-1.png │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ └── unnamed-chunk-6-2.png │ │ ├── a03_example_spatial_visium.html │ │ ├── a03_example_spatial_visium_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-4-1.png │ │ │ │ └── unnamed-chunk-8-1.png │ │ ├── a04_example_spatial_slideseqV2.html │ │ ├── a04_example_spatial_slideseqV2_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-4-1.png │ │ │ │ └── unnamed-chunk-8-1.png │ │ ├── a05_moca_100k.html │ │ ├── a06_pseudotime.html │ │ ├── a07_gene_sets.html │ │ ├── a07_gene_sets_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-4-1.png │ │ │ │ └── unnamed-chunk-7-1.png │ │ ├── a08_gene_clustering.html │ │ ├── a08_gene_clustering_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-11-1.png │ │ │ │ ├── unnamed-chunk-14-1.png │ │ │ │ ├── unnamed-chunk-16-1.png │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ ├── unnamed-chunk-6-2.png │ │ │ │ └── unnamed-chunk-8-1.png │ │ └── figures │ │ │ ├── a05-plot_dim-1.png │ │ │ ├── a05-plot_results-1.png │ │ │ ├── a06-plot_cells_1-1.png │ │ │ ├── a06-plot_cells_2-1.png │ │ │ ├── a06-plot_cells_2-2.png │ │ │ ├── a06-plot_cells_3-1.png │ │ │ ├── a06-plot_cells_4-1.png │ │ │ ├── a06-plot_cells_5-1.png │ │ │ ├── a06-plot_genes_1-1.png │ │ │ ├── a06-plot_genes_2-1.png │ │ │ ├── a06-plot_genes_2-2.png │ │ │ ├── a06-plot_haystack_1-1.png │ │ │ ├── a06-plot_haystack_1-2.png │ │ │ ├── a06-plot_haystack_2-1.png │ │ │ ├── a06-plot_haystack_3-1.png │ │ │ └── a06-plot_pca-1.png │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── dat.expression.html │ ├── dat.tsne.html │ ├── default_bandwidth.nrd.html │ ├── extract_row_dgRMatrix.html │ ├── extract_row_lgRMatrix.html │ ├── figures │ │ ├── README-example3-1.png │ │ └── README-example5-1.png │ ├── get_D_KL.html │ ├── get_D_KL_continuous_highD.html │ ├── get_D_KL_highD.html │ ├── get_density.html │ ├── get_dist_two_sets.html │ ├── get_euclidean_distance.html │ ├── get_grid_points.html │ ├── get_log_p_D_KL.html │ ├── get_log_p_D_KL_continuous.html │ ├── get_parameters_haystack.html │ ├── get_reference.html │ ├── haystack.html │ ├── haystack_2D.html │ ├── haystack_continuous_highD.html │ ├── haystack_highD.html │ ├── hclust_haystack.html │ ├── hclust_haystack_highD.html │ ├── hclust_haystack_raw.html │ ├── index.html │ ├── kde2d_faster.html │ ├── kmeans_haystack.html │ ├── kmeans_haystack_highD.html │ ├── kmeans_haystack_raw.html │ ├── plot_compare_ranks.html │ ├── plot_gene_haystack.html │ ├── plot_gene_haystack_raw.html │ ├── plot_gene_set_haystack.html │ ├── plot_gene_set_haystack_raw.html │ ├── plot_rand_KLD.html │ ├── plot_rand_fit.html │ ├── read_haystack.html │ ├── show_result_haystack.html │ ├── singleCellHaystack-package.html │ └── write_haystack.html └── sitemap.xml ├── inst └── CITATION ├── man ├── dat.expression.Rd ├── dat.tsne.Rd ├── default_bandwidth.nrd.Rd ├── extract_row_dgRMatrix.Rd ├── extract_row_lgRMatrix.Rd ├── figures │ ├── README-example3-1.png │ └── README-example5-1.png ├── get_D_KL.Rd ├── get_D_KL_continuous_highD.Rd ├── get_D_KL_highD.Rd ├── get_density.Rd ├── get_dist_two_sets.Rd ├── get_euclidean_distance.Rd ├── get_grid_points.Rd ├── get_log_p_D_KL.Rd ├── get_log_p_D_KL_continuous.Rd ├── get_parameters_haystack.Rd ├── get_reference.Rd ├── haystack.Rd ├── haystack_2D.Rd ├── haystack_continuous_highD.Rd ├── haystack_highD.Rd ├── hclust_haystack.Rd ├── hclust_haystack_highD.Rd ├── hclust_haystack_raw.Rd ├── kde2d_faster.Rd ├── kmeans_haystack.Rd ├── kmeans_haystack_highD.Rd ├── kmeans_haystack_raw.Rd ├── plot_compare_ranks.Rd ├── plot_gene_haystack.Rd ├── plot_gene_haystack_raw.Rd ├── plot_gene_set_haystack.Rd ├── plot_gene_set_haystack_raw.Rd ├── plot_rand_KLD.Rd ├── plot_rand_fit.Rd ├── read_haystack.Rd ├── show_result_haystack.Rd ├── singleCellHaystack-package.Rd └── write_haystack.Rd ├── singleCellHaystack.Rproj ├── tests ├── testthat.R └── testthat │ ├── test-extract_row.R │ ├── test-haystack_continuous.R │ └── test-haystack_sparse.R └── vignettes ├── .gitignore ├── a01_toy_example.Rmd └── examples ├── a02_example_scRNAseq.Rmd ├── a03_example_spatial_visium.Rmd ├── a04_example_spatial_slideseqV2.Rmd ├── a05_moca_100k.Rmd ├── a06_pseudotime.Rmd ├── a07_gene_sets.Rmd ├── a08_gene_clustering.Rmd └── figures ├── a05-plot_dim-1.png ├── a05-plot_results-1.png ├── a06-plot_cells_1-1.png ├── a06-plot_cells_2-1.png ├── a06-plot_cells_2-2.png ├── a06-plot_cells_3-1.png ├── a06-plot_cells_4-1.png ├── a06-plot_cells_5-1.png ├── a06-plot_genes_1-1.png ├── a06-plot_genes_2-1.png ├── a06-plot_genes_2-2.png ├── a06-plot_haystack_1-1.png ├── a06-plot_haystack_1-2.png ├── a06-plot_haystack_2-1.png ├── a06-plot_haystack_3-1.png └── 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