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 changes were made to
                        this function.
extract_row_dgRMatrix   Returns a row of a sparse matrix of class
                        dgRMatrix. Function made by Ben Bolker and Ott
                        Toomet (see
                        https://stackoverflow.com/questions/47997184/)
extract_row_lgRMatrix   Returns a row of a sparse matrix of class
                        lgRMatrix. Function made by Ben Bolker and Ott
                        Toomet (see
                        https://stackoverflow.com/questions/47997184/)
get_D_KL                Calculates the Kullback-Leibler divergence
                        between distributions.
get_D_KL_continuous_highD
                        Calculates the Kullback-Leibler divergence
                        between distributions for the high-dimensional
                        continuous version of haystack.
get_D_KL_highD          Calculates the Kullback-Leibler divergence
                        between distributions for the high-dimensional
                        version of haystack().
get_density             Function to get the density of points with
                        value TRUE in the (x,y) plot
get_dist_two_sets       Calculate the pairwise Euclidean distances
                        between the rows of 2 matrices.
get_euclidean_distance
                        Calculate the Euclidean distance between x and
                        y.
get_grid_points         A function to decide grid points in a
                        higher-dimensional space
get_log_p_D_KL          Estimates the significance of the observed
                        Kullback-Leibler divergence by comparing to
                        randomizations.
get_log_p_D_KL_continuous
                        Estimates the significance of the observed
                        Kullback-Leibler divergence by comparing to
                        randomizations for the continuous version of
                        haystack.
get_parameters_haystack
                        Function that decides most of the parameters
                        that will be used during the "Haystack"
                        analysis.
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 continuous
                        expression levels.
haystack_highD          The main Haystack function, for
                        higher-dimensional spaces.
hclust_haystack         Function for hierarchical clustering of genes
                        according to their expression distribution in
                        2D or multi-dimensional space
hclust_haystack_highD   Function for hierarchical clustering of genes
                        according to their distribution in a
                        higher-dimensional space.
hclust_haystack_raw     Function for hierarchical clustering of genes
                        according to their distribution on a 2D plot.
kde2d_faster            Based on the MASS kde2d() function, but heavily
                        simplified; it's just tcrossprod() now.
kmeans_haystack         Function for k-means clustering of genes
                        according to their expression distribution in
                        2D or multi-dimensional space
kmeans_haystack_highD   Function for k-means clustering of genes
                        according to their distribution in a
                        higher-dimensional space.
kmeans_haystack_raw     Function for k-means clustering of genes
                        according to their distribution on a 2D plot.
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 2D plot
plot_gene_set_haystack_raw
                        Visualizing the detection/expression of a set
                        of genes in a 2D plot
plot_rand_KLD           plot_rand_KLD
plot_rand_fit           plot_rand_fit
read_haystack           Function to read haystack results from file.
show_result_haystack    show_result_haystack
write_haystack          Function to write haystack result data to file.
