Man pages for singleCellHaystack
Finding Needles (=differentially Expressed Genes) in Haystacks (=single Cell Data)

dat.expressionSingle cell RNA-seq dataset.
dat.tsneSingle cell tSNE coordingates.
default_bandwidth.nrdDefault function given by function bandwidth.nrd in MASS. No...
extract_row_dgRMatrixReturns a row of a sparse matrix of class dgRMatrix. Function...
extract_row_lgRMatrixReturns a row of a sparse matrix of class lgRMatrix. Function...
get_densityFunction to get the density of points with value TRUE in the...
get_dist_two_setsCalculate the pairwise Euclidean distances between the rows...
get_D_KLCalculates the Kullback-Leibler divergence between...
get_D_KL_highDCalculates the Kullback-Leibler divergence between...
get_euclidean_distanceCalculate the Euclidean distance between x and y.
get_grid_pointsA function to decide grid points in a higher-dimensional...
get_log_p_D_KLEstimates the significance of the observed Kullback-Leibler...
get_parameters_haystackFunction that decides most of the parameters that will be...
get_referenceGet reference distribution
haystackThe main Haystack function
haystack_2DThe main Haystack function, for 2-dimensional spaces.
haystack_highDThe main Haystack function, for higher-dimensional spaces.
hclust_haystackFunction for hierarchical clustering of genes according to...
hclust_haystack_highDFunction for hierarchical clustering of genes according to...
hclust_haystack_rawFunction for hierarchical clustering of genes according to...
kde2d_fasterBased on the MASS kde2d() function, but heavily simplified;...
kmeans_haystackFunction for k-means clustering of genes according to their...
kmeans_haystack_highDFunction for k-means clustering of genes according to their...
kmeans_haystack_rawFunction for k-means clustering of genes according to their...
plot_gene_haystackVisualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack_rawVisualizing the detection/expression of a gene in a 2D plot
plot_gene_set_haystackVisualizing the detection/expression of a set of genes in a...
plot_gene_set_haystack_rawVisualizing the detection/expression of a set of genes in a...
read_haystackFunction to read haystack results from file.
show_result_haystackShows the results of the 'haystack' analysis in various ways,...
singleCellHaystack-packagesingleCellHaystack: Finding Needles (=differentially...
write_haystackFunction to write haystack result data to file.
singleCellHaystack documentation built on March 28, 2021, 9:12 a.m.