R: A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data

# A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data

## Documentation for package ‘singleCellHaystack’ version 1.0.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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_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_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_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.data.frame | The main Haystack function
haystack.matrix | The main Haystack function
haystack.Seurat | The main Haystack function
haystack.SingleCellExperiment | 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.data.frame | Function for hierarchical clustering of genes according to their expression distribution in 2D or multi-dimensional space
hclust_haystack.matrix | 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.data.frame | Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space
kmeans_haystack.matrix | 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.data.frame | Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack.matrix | Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack.Seurat | Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack.SingleCellExperiment | 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.data.frame | Visualizing the detection/expression of a set of genes in a 2D plot
plot_gene_set_haystack.matrix | Visualizing the detection/expression of a set of genes in a 2D plot
plot_gene_set_haystack.Seurat | Visualizing the detection/expression of a set of genes in a 2D plot
plot_gene_set_haystack.SingleCellExperiment | 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_fit | plot_rand_fit
plot_rand_fit.haystack | plot_rand_fit
plot_rand_KLD | plot_rand_KLD
read_haystack | Function to read haystack results from file.
show_result_haystack | show_result_haystack
show_result_haystack.haystack | show_result_haystack
write_haystack | Function to write haystack result data to file.