Single Cell Overview of Normalized Expression data

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Documentation for package ‘scone’ version 1.12.0

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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