# Bayesian Analysis of Single-Cell Sequencing data

## Documentation for package ‘BASiCS’ version 1.4.0

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

## Help Pages

BASiCS-deprecated | Deprecated functions in package 'BASiCS'
BASiCS_Chain | The BASiCS_Chain class
BASiCS_Chain-class | The BASiCS_Chain class
BASiCS_Chain-methods | 'show' method for BASiCS_Chain objects
BASiCS_DenoisedCounts | Calculates denoised expression expression counts
BASiCS_DenoisedRates | Calculates denoised expression rates
BASiCS_DetectHVG | Detection method for highly and lowly variable genes
BASiCS_DetectHVG_LVG | Detection method for highly and lowly variable genes
BASiCS_DetectLVG | Detection method for highly and lowly variable genes
BASiCS_D_TestDE | Detection of genes with changes in expression.
BASiCS_Filter | Filter for input datasets
BASiCS_LoadChain | Loads pre-computed MCMC chains generated by the 'BASiCS_MCMC' function
BASiCS_MCMC | BASiCS MCMC sampler
BASiCS_showFit | Plotting the trend after Bayesian regression
BASiCS_showFit-BASiCS_Chain-method | Plotting the trend after Bayesian regression
BASiCS_showFit-method | Plotting the trend after Bayesian regression
BASiCS_Sim | Generates synthetic data according to the model implemented in BASiCS
BASiCS_Summary | The BASiCS_Summary class
BASiCS_Summary-class | The BASiCS_Summary class
BASiCS_Summary-methods | 'show' method for BASiCS_Summary objects
BASiCS_TestDE | Detection of genes with changes in expression
BASiCS_VarianceDecomp | Decomposition of gene expression variability according to BASiCS
BASiCS_VarThresholdSearchHVG | Detection method for highly and lowly variable genes using a grid of variance contribution thresholds
BASiCS_VarThresholdSearchHVG_LVG | Detection method for highly and lowly variable genes using a grid of variance contribution thresholds
BASiCS_VarThresholdSearchLVG | Detection method for highly and lowly variable genes using a grid of variance contribution thresholds
ChainRNA | Extract from the chain obtained for the Grun et al (2014) data: pool-and-split samples
ChainRNAReg | Extract from the chain obtained for the Grun et al (2014) data: pool-and-split samples (regression model)
ChainSC | Extract from the chain obtained for the Grun et al (2014) data: single-cell samples
ChainSCReg | Extract from the chain obtained for the Grun et al (2014) data: single-cell samples (regression model)
colnames | 'colnames' method for BASiCS_Chain objects
colnames-method | 'colnames' method for BASiCS_Chain objects
displayChainBASiCS | Accessors for the slots of a BASiCS_Chain object
displayChainBASiCS-BASiCS_Chain-method | Accessors for the slots of a BASiCS_Chain object
displayChainBASiCS-method | Accessors for the slots of a BASiCS_Chain object
displaySummaryBASiCS | Accessors for the slots of a 'BASiCS_Summary' object
displaySummaryBASiCS-BASiCS_Summary-method | Accessors for the slots of a 'BASiCS_Summary' object
displaySummaryBASiCS-method | Accessors for the slots of a 'BASiCS_Summary' object
makeExampleBASiCS_Data | Create a synthetic SingleCellExperiment example object with the format required for BASiCS
newBASiCS_Chain | Creates a BASiCS_Chain object from pre-computed MCMC chains
newBASiCS_Data | Creates a SingleCellExperiment object from a matrix of expression counts and experimental information about spike-in genes
plot | 'plot' method for BASiCS_Chain objects
plot,BASiCS_Summary-method, | 'plot' method for BASiCS_Summary objects
plot-BASiCS_Chain-method | 'plot' method for BASiCS_Chain objects
plot-BASiCS_Summary-method | 'plot' method for BASiCS_Summary objects
plot-method | 'plot' method for BASiCS_Chain objects
plot-method | 'plot' method for BASiCS_Summary objects
rownames | 'rownames' method for BASiCS_Chain objects
rownames-method | 'rownames' method for BASiCS_Chain objects
show-method | 'show' method for BASiCS_Chain objects
show-method | 'show' method for BASiCS_Summary objects
subset | A 'subset' method for 'BASiCS_Chain" objects
subset-method | A 'subset' method for 'BASiCS_Chain" objects
Summary | 'Summary' method for BASiCS_Chain objects
Summary-method | 'Summary' method for BASiCS_Chain objects
updateObject-method | 'show' method for BASiCS_Chain objects