# Single Cell Overview of Normalized Expression data

## Documentation for package ‘scone’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.
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