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