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

calc_bins2regionsConverts list of bins from binning scheme to regions.
calc_centroareasCalculates centromere regions (areas).
calc_pinmatSelect features and generate the incidence table.
calc_ploidiesCalculates ploidies for samples passed in 'segment_df'.
calc_regions2binsConverts regions to list of bins from binning scheme.
case_filenamesConstructs names for various output files based on...
chrom_numericConverts chrom name to numeric and adds 'chrom.numeric'...
find_clonesIdentify nodes in a hierarchical tree which qualify as...
find_subclonesIdentify subclones in a clonal branch of a hierarchical tree.
fisher_distCalculates a distance matrix given Fisher FDR true p-values.
fisher_fdrCompute FDRs for Fisher's test p-values.
hclust_treeBuild the hierarchical clustering tree.
segment_varbin_filesGenerate the segmented profile for each cell.
sgains_pipelineIntegration with 'sGAINS' tool.
sim_fisher_wrapperSimulate the Fisher's test p-values.
tree_pyBuilds HC tree representation based on the distance matrix...
varbin_input_filesCollects all bin count files from given directory
KrasnitzLab/SCclust documentation built on Dec. 12, 2018, 8:44 p.m.