.generateSubsets        Generate balanced subsets for divide and
                        conquer BASiCS
BASiCS-defunct          Defunct functions in package 'BASiCS'
BASiCS_CalculateERCC    Convert concentration in moles per microlitre
                        to molecule counts
BASiCS_Chain            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_DetectVG         Detection method for highly (HVG) and lowly
                        (LVG) variable genes
BASiCS_DiagHist         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_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-class
                        object.
BASiCS_PlotDE           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_PlotVarianceDecomp
                        Plot variance decomposition results.
BASiCS_PriorParam       Prior parameters for BASiCS_MCMC
BASiCS_Result           The BASiCS_Result class
BASiCS_ResultDE         The BASiCS_ResultDE class
BASiCS_ResultVG         The BASiCS_ResultVG class
BASiCS_ResultsDE        The BASiCS_ResultsDE class
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-methods
                        'show' method for BASiCS_Summary objects
BASiCS_TestDE           Detection of genes with changes in expression
BASiCS_VarThresholdSearchHVG
                        Detection method for highly and lowly variable
                        genes using a grid of variance contribution
                        thresholds
BASiCS_VarianceDecomp   Decomposition of gene expression variability
                        according to BASiCS
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)
Summary                 'Summary' method for BASiCS_Chain objects
[,BASiCS_ResultsDE,ANY,ANY,ANY-method
                        Methods for subsetting BASiCS_Result and
                        BASiCS_ResultsDE objects.
as.data.frame,BASiCS_ResultsDE-method
                        Converting BASiCS results objects to
                        data.frames
dim                     'dim' method for BASiCS_Chain objects
dimnames                'dimnames' method for BASiCS_Chain objects
displayChainBASiCS-BASiCS_Chain-method
                        Accessors for the slots of a BASiCS_Chain
                        object
displaySummaryBASiCS-BASiCS_Summary-method
                        Accessors for the slots of a 'BASiCS_Summary'
                        object
format,BASiCS_ResultsDE-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_Chain-method
                        'plot' method for BASiCS_Chain objects
plot-BASiCS_Summary-method
                        'plot' method for BASiCS_Summary objects
rowData,BASiCS_ResultsDE-method
                        rowData getter and setter for BASiCS_ResultsDE
                        and BASiCS_ResultVG objects.
show,BASiCS_ResultDE-method
                        Accessors for the slots of a 'BASiCS_ResultDE'
                        object
show,BASiCS_ResultVG-method
                        Accessors for the slots of a 'BASiCS_ResultVG'
                        object
show,BASiCS_ResultsDE-method
                        Accessors for the slots of a 'BASiCS_ResultsDE'
                        object
subset                  A 'subset' method for 'BASiCS_Chain" objects
