Man pages for kieranrcampbell/clonealign
Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq
| clonealign | Assign scRNA-seq to clone-of-origin |
| clone_assignment | Computes map clone assignment given EM object |
| compute_ca_fit_mse | Compute mean squared error of a clonealign fit |
| compute_correlations | Post-hoc compute correlations between copy number and... |
| construct_ai_likelihood | Construct allele specific complete data likelihood |
| df_cnv | Example raw copy number data |
| example_clonealign_fit | Example clonealign_fit |
| example_sce | Example SingleCellExperiment |
| get_outlying_genes | Get outlier genes |
| inference_tflow | EM inference with tensorflow |
| plot_clonealign | Plot gene expression and copy number |
| preprocess_for_clonealign | Preprocess data for input to clonealign |
| print.clonealign_fit | Print a clonealign_fit |
| process_cnv_data | Preprocess copy number data |
| process_gene_expression_data | Check and pre-process gene expression data |
| recompute_clone_assignment | Re-computes map clone assignment at a given threshold |
| round2 | Round a number to two significant figures |
| run_clonealign | Run clonealign across a range of initializations |
| saturate | Saturate a copy number matrix above a certain threshold |
