Man pages for seqpipe/SCclust
Clustering of Single Cell Sequencing Copy Number Profiles to Identify Clones
| 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 |
