CLR_FN                  Centered log-ratio (CLR) normalization wrapper
                        function
DESEQ_FN                Relative log-expression (RLE; DESeq) scaling
                        normalization wrapper function
FQ_FN                   Full-quantile normalization wrapper function
PSINORM_FN              PsiNorm normalization wrapper
PsiNorm                 PsiNorm: scaling normalization based on the
                        Pareto distribution
SCRAN_FN                Simple deconvolution normalization wrapper
SUM_FN                  Sum scaling normalization function
SconeExperiment-class   Class SconeExperiment
TMM_FN                  Weighted trimmed mean of M-values (TMM) scaling
                        normalization wrapper function
UQ_FN                   Upper-quartile (UQ) scaling normalization
                        wrapper function
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
control_genes           Data: Positive and Negative Control Genes
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
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 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
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
select_methods          Get a subset of normalizations from a
                        SconeExperiment object
simple_FNR_params       Fit Simple False-Negative Model
