dat.expression | Single cell RNA-seq dataset. |
dat.tsne | Single cell tSNE coordingates. |
default_bandwidth.nrd | Default function given by function bandwidth.nrd in MASS. No... |
extract_row_dgRMatrix | Returns a row of a sparse matrix of class dgRMatrix. Function... |
extract_row_lgRMatrix | Returns a row of a sparse matrix of class lgRMatrix. Function... |
get_density | Function to get the density of points with value TRUE in the... |
get_dist_two_sets | Calculate the pairwise Euclidean distances between the rows... |
get_D_KL | Calculates the Kullback-Leibler divergence between... |
get_D_KL_continuous_highD | Calculates the Kullback-Leibler divergence between... |
get_D_KL_highD | Calculates the Kullback-Leibler divergence between... |
get_euclidean_distance | Calculate the Euclidean distance between x and y. |
get_grid_points | A function to decide grid points in a higher-dimensional... |
get_log_p_D_KL | Estimates the significance of the observed Kullback-Leibler... |
get_log_p_D_KL_continuous | Estimates the significance of the observed Kullback-Leibler... |
get_parameters_haystack | Function that decides most of the parameters that will be... |
get_reference | Get reference distribution |
haystack | The main Haystack function |
haystack_2D | The main Haystack function, for 2-dimensional spaces. |
haystack_continuous_highD | The main Haystack function, for higher-dimensional spaces and... |
haystack_highD | The main Haystack function, for higher-dimensional spaces. |
hclust_haystack | Function for hierarchical clustering of genes according to... |
hclust_haystack_highD | Function for hierarchical clustering of genes according to... |
hclust_haystack_raw | Function for hierarchical clustering of genes according to... |
kde2d_faster | Based on the MASS kde2d() function, but heavily simplified;... |
kmeans_haystack | Function for k-means clustering of genes according to their... |
kmeans_haystack_highD | Function for k-means clustering of genes according to their... |
kmeans_haystack_raw | Function for k-means clustering of genes according to their... |
plot_compare_ranks | plot_compare_ranks |
plot_gene_haystack | Visualizing the detection/expression of a gene in a 2D plot |
plot_gene_haystack_raw | Visualizing the detection/expression of a gene in a 2D plot |
plot_gene_set_haystack | Visualizing the detection/expression of a set of genes in a... |
plot_gene_set_haystack_raw | Visualizing the detection/expression of a set of genes in a... |
plot_rand_fit | plot_rand_fit |
plot_rand_KLD | plot_rand_KLD |
read_haystack | Function to read haystack results from file. |
show_result_haystack | show_result_haystack |
singleCellHaystack-package | singleCellHaystack: A Universal Differential Expression... |
write_haystack | Function to write haystack result data to file. |
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