# Bayesian Analysis of Single-Cell Sequencing data

## Documentation for package ‘BASiCS’ version 2.2.0

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

## Help Pages

.generateSubsets | Generate balanced subsets for divide and conquer BASiCS
as.data.frame-method | Converting BASiCS results objects to data.frames
BASiCS-defunct | Defunct 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_CorrectOffset | Remove global mean expression offset
BASiCS_DenoisedCounts | Calculates denoised expression expression counts
BASiCS_DenoisedRates | Calculates denoised expression rates
BASiCS_DetectHVG | Detection method for highly (HVG) and lowly (LVG) variable genes
BASiCS_DetectHVGLVG | Detection method for highly (HVG) and lowly (LVG) variable genes
BASiCS_DetectHVG_LVG | Detection method for highly (HVG) and lowly (LVG) variable genes
BASiCS_DetectLVG | Detection method for highly (HVG) and lowly (LVG) variable genes
BASiCS_DetectVG | Detection method for highly (HVG) and lowly (LVG) variable genes
BASiCS_DiagHist | Create diagnostic plots of MCMC parameters
BASiCS_diagHist | Create diagnostic plots of MCMC parameters
BASiCS_DiagPlot | Create diagnostic plots of MCMC parameters
BASiCS_diagPlot | Create diagnostic plots of MCMC parameters
BASiCS_DivideAndConquer | Run divide and conquer MCMC with BASiCS
BASiCS_Draw | Generate a draw from the posterior of BASiCS using the generative model.
BASiCS_D_TestDE | Defunct functions in package 'BASiCS'
BASiCS_EffectiveSize | Calculate effective sample size for BASiCS_Chain parameters
BASiCS_effectiveSize | Calculate effective sample size for BASiCS_Chain parameters
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_MockSCE | Create a mock SingleCellExperiment object.
BASiCS_PlotDE | Produce plots assessing differential expression results
BASiCS_PlotDE-method | Produce plots assessing differential expression results
BASiCS_PlotOffset | Visualise global offset in mean expression between two chains.
BASiCS_PlotVG | Plots of HVG/LVG search.
BASiCS_PriorParam | Prior parameters for BASiCS_MCMC
BASiCS_Result | The BASiCS_Result class
BASiCS_Result-class | The BASiCS_Result class
BASiCS_ResultDE | The BASiCS_ResultDE class
BASiCS_ResultDE-class | The BASiCS_ResultDE class
BASiCS_ResultsDE | The BASiCS_ResultsDE class
BASiCS_ResultsDE-class | The BASiCS_ResultsDE class
BASiCS_ResultVG | The BASiCS_ResultVG class
BASiCS_ResultVG-class | The BASiCS_ResultVG class
BASiCS_ShowFit | Plotting the trend after Bayesian regression
BASiCS_showFit | 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
BASiCS_VarThresholdSearchVG | 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)
dim | 'dim' method for BASiCS_Chain objects
dim-method | 'dim' method for BASiCS_Chain objects
dimnames | 'dimnames' method for BASiCS_Chain objects
dimnames-method | 'dimnames' 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
format-method | Methods for formatting BASiCS_Result and BASiCS_ResultsDE objects.
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,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
rowData-method | rowData getter and setter for BASiCS_ResultsDE and BASiCS_ResultVG objects.
rowData<--method | rowData getter and setter for BASiCS_ResultsDE and BASiCS_ResultVG objects.
show-method | 'show' method for BASiCS_Chain objects
show-method | 'show' method for BASiCS_Summary objects
show-method | Accessors for the slots of a 'BASiCS_ResultDE' object
show-method | Accessors for the slots of a 'BASiCS_ResultVG' object
show-method | Accessors for the slots of a 'BASiCS_ResultsDE' object
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
[-method | Methods for subsetting BASiCS_Result and BASiCS_ResultsDE objects.
[[-method | Methods for subsetting BASiCS_Result and BASiCS_ResultsDE objects.