Man pages for YosefLab/scone
Single Cell Overview of Normalized Expression data

biplot_colorFunction for biplotting with no point labels and with points...
biplot_interactiveInteractive biplot
CLR_FNCentered log-ratio (CLR) normalization wrapper function
control_genesData: Positive and Negative Control Genes
DESEQ_FNRelative log-expression (RLE; DESeq) scaling normalization...
estimate_ziberParameter estimation of zero-inflated bernoulli model
factor_sample_filterFactor-based Sample Filtering: Function to filter single-cell...
fast_estimate_ziberFast parameter estimation of zero-inflated bernoulli model
FQ_FNFull-quantile normalization wrapper function
get_bioGet Factor of Biological Conditions and Batch
get_designRetrieve Design Matrix
get_negconruvGet Negative and Positive Controls
get_normalizedRetrieve Normalized Matrix
get_paramsExtract scone parameters
get_qcGet Quality Control Matrix
get_scoresExtract scone scores
impute_expectationImputation of zero abundance based on general zero-inflated...
impute_nullNull or no-op imputation
lm_adjustLinear Adjustment Normalization
make_designMake a Design Matrix
metric_sample_filterMetric-based Sample Filtering: Function to filter single-cell...
sconeNormalize Expression Data and Evaluate Normalization...
scone_easybakeWrapper for Running Essential SCONE Modules
SconeExperiment-classClass SconeExperiment
sconeReportSCONE Report Browser: Browse Evaluation of Normalization...
score_matrixSCONE Evaluation: Evaluate an Expression Matrix
SCRAN_FNSimple deconvolution normalization wrapper
select_methodsGet a subset of normalizations from a SconeExperiment object
simple_FNR_paramsFit Simple False-Negative Model
SUM_FNSum scaling normalization function
TMM_FNWeighted trimmed mean of M-values (TMM) scaling normalization...
UQ_FNUpper-quartile (UQ) scaling normalization wrapper function
YosefLab/scone documentation built on Nov. 8, 2017, 2:06 a.m.