calc_bins2regions | Converts list of bins from binning scheme to regions. |
calc_centroareas | Calculates centromere regions (areas). |
calc_pinmat | Select features and generate the incidence table. |
calc_ploidies | Calculates ploidies for samples passed in 'segment_df'. |
calc_regions2bins | Converts regions to list of bins from binning scheme. |
case_filenames | Constructs names for various output files based on... |
chrom_numeric | Converts chrom name to numeric and adds 'chrom.numeric'... |
find_clones | Identify nodes in a hierarchical tree which qualify as... |
find_subclones | Identify subclones in a clonal branch of a hierarchical tree. |
fisher_dist | Calculates a distance matrix given Fisher FDR true p-values. |
fisher_fdr | Compute FDRs for Fisher's test p-values. |
hclust_tree | Build the hierarchical clustering tree. |
segment_varbin_files | Generate the segmented profile for each cell. |
sgains_pipeline | Integration with 'sGAINS' tool. |
sim_fisher_wrapper | Simulate the Fisher's test p-values. |
tree_py | Builds HC tree representation based on the distance matrix... |
varbin_input_files | Collects all bin count files from given directory |
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