tl module

Helpful tools

PIC_BGdoubletsOEratios	Generate distribution of O/E ratios for colocalization probabilities of cell type pairs in randomly generated doublets (background dist) for tests in PIC-seq data
PIC_BGdoubletsOEratios_parallel	Generate one set of O/E ratios for cell type pair co-localization probabilities from randomly paired single cells.
assign_properties	Assign properties to network g to visualize with gravis interactive networks
cellCatContained	Generate boolean element indicating whether the specified element (cell pair) is contained in a list (category)
cells_niche_colors	Make dataframe of cell types with their corresponding niches and colors
compute_network_stats	Compute standard centrality statistics for a (signed) NetworkX graph.
downsample_class	Reduce the number of elements belonging to target_class by a given factor.
getColocFilter	Get filtering object indicating which cell pairs are differentially co-localized
getExpectedColocProbsFromSCs	Compute the expected co-localization probability of each cell type pair by multiplying cell type proportions derived from single-cell (singlets) data.
get_PIC_BG_OEratios_DF	Generate nreps sets of O/E ratios for cell type pair co-localization probabilities by running PIC_BGdoubletsOEratios_parallel() in parallel.
get_pairCatDFdir	Get dataframe of cell pair to niche pair correspondence
get_spatial_radius_BG_OEratios_DF	Optimized version of get_spatial_radius_BG_OEratios_DF using sparse matrix multiplication.
get_spot_ct_props	Get cell type proportions per spot by summing the probabilities of cells of the same kind in each spot
plot_top_stats	Bar plots of the top nodes by betweenness, PageRank, and signed degree centrality.
processCTKRoutput	Remove suffixes '|L' , '|R' and '|TF' from cell - cell communication (CrossTalkeR) tables
pval_filtered_HMdf	Get dataframe for scores heatmap from dataframe obtained from diffColoc_test()
unique	get unique elements in array without re-sorting