| biplot_color | Function for biplotting with no point labels and with points color-coded according to a quantitative variable. For example: the rank of normalization performance. |
| biplot_interactive | Interactive biplot |
| cellcycle_genes | Data: Positive and Negative Control Genes |
| CLR_FN | Centered log-ratio (CLR) normalization wrapper function |
| control_genes | Data: Positive and Negative Control Genes |
| cortical_markers | Data: Positive and Negative Control Genes |
| DESEQ_FN | Relative log-expression (RLE; DESeq) scaling normalization wrapper function |
| estimate_ziber | Parameter estimation of zero-inflated bernoulli model |
| factor_sample_filter | Factor-based Sample Filtering: Function to filter single-cell RNA-Seq libraries. |
| fast_estimate_ziber | Fast parameter estimation of zero-inflated bernoulli model |
| FQT_FN | Full-quantile normalization wrapper function |
| FQ_FN | Full-quantile normalization wrapper function |
| get_batch | Get Factor of Biological Conditions and Batch |
| get_batch-method | Get Factor of Biological Conditions and Batch |
| get_bio | Get Factor of Biological Conditions and Batch |
| get_bio-method | Get Factor of Biological Conditions and Batch |
| get_design | Retrieve Design Matrix |
| get_design-method | Retrieve Design Matrix |
| get_negconeval | Get Negative and Positive Controls |
| get_negconeval-method | Get Negative and Positive Controls |
| get_negconruv | Get Negative and Positive Controls |
| get_negconruv-method | Get Negative and Positive Controls |
| get_normalized | Retrieve Normalized Matrix |
| get_normalized-method | Retrieve Normalized Matrix |
| get_params | Extract scone parameters |
| get_params-method | Extract scone parameters |
| get_poscon | Get Negative and Positive Controls |
| get_poscon-method | Get Negative and Positive Controls |
| get_qc | Get Quality Control Matrix |
| get_qc-method | Get Quality Control Matrix |
| get_scores | Extract scone scores |
| get_scores-method | Extract scone scores |
| get_score_ranks | Extract scone scores |
| get_score_ranks-method | Extract scone scores |
| housekeeping | Data: Positive and Negative Control Genes |
| housekeeping_revised | Data: Positive and Negative Control Genes |
| impute_expectation | Imputation of zero abundance based on general zero-inflated model |
| 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 RNA-Seq libraries. |
| PsiNorm | PsiNorm: scaling normalization based on the Pareto distribution |
| PsiNorm-method | PsiNorm: scaling normalization based on the Pareto distribution |
| PSINORM_FN | PsiNorm normalization wrapper |
| scone | Normalize Expression Data and Evaluate Normalization Performance |
| scone-method | Normalize Expression Data and Evaluate Normalization Performance |
| SconeExperiment | Class SconeExperiment |
| SconeExperiment-class | Class SconeExperiment |
| SconeExperiment-method | Class SconeExperiment |
| sconeReport | SCONE Report Browser: Browse Evaluation of Normalization Performance |
| scone_easybake | Wrapper for Running Essential SCONE Modules |
| 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 |
| select_methods-method | 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 wrapper function |
| UQ_FN | Upper-quartile (UQ) scaling normalization wrapper function |