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. |
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. |
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 |