Man pages for YosefLab/scone
Single Cell Overview of Normalized Expression data
| biplot_color | Function for biplotting with no point labels and with points... |
| biplot_interactive | Interactive biplot |
| CLR_FN | Centered log-ratio (CLR) normalization wrapper function |
| control_genes | Data: Positive and Negative Control Genes |
| DESEQ_FN | Relative log-expression (RLE; DESeq) scaling normalization... |
| dot-likfn | Likelihood Function of the Logistic Model |
| dot-parse_row | Parse rows |
| dot-pzfn | Posterior probability of detection |
| estimate_ziber | Parameter estimation of zero-inflated bernoulli model |
| factor_sample_filter | Factor-based Sample Filtering: Function to filter single-cell... |
| fast_estimate_ziber | Fast parameter estimation of zero-inflated bernoulli model |
| FQ_FN | Full-quantile normalization wrapper function |
| get_bio | Get Factor of Biological Conditions and Batch |
| get_design | Retrieve Design Matrix |
| get_negconruv | Get Negative and Positive Controls |
| get_normalized | Retrieve Normalized Matrix |
| get_params | Extract scone parameters |
| get_qc | Get Quality Control Matrix |
| get_scores | Extract scone scores |
| impute_expectation | Imputation of zero abundance based on general zero-inflated... |
| impute_null | Null or no-op imputation |
| lm_adjust | Linear Adjustment Normalization |
| make_design | Make a Design Matrix |
| metric_sample_filter | Metric-based Sample Filtering: Function to filter single-cell... |
| PsiNorm | PsiNorm: scaling normalization based on the Pareto... |
| PSINORM_FN | PsiNorm normalization wrapper |
| scone | Normalize Expression Data and Evaluate Normalization... |
| scone_easybake | Wrapper for Running Essential SCONE Modules |
| SconeExperiment-class | Class SconeExperiment |
| sconeReport | SCONE Report Browser: Browse Evaluation of Normalization... |
| score_matrix | SCONE Evaluation: Evaluate an Expression Matrix |
| SCRAN_FN | Simple deconvolution normalization wrapper |
| select_methods | Get a subset of normalizations from a SconeExperiment object |
| simple_FNR_params | Fit Simple False-Negative Model |
| SUM_FN | Sum scaling normalization function |
| TMM_FN | Weighted trimmed mean of M-values (TMM) scaling normalization... |
| UQ_FN | Upper-quartile (UQ) scaling normalization wrapper function |
