Bayesian Analysis of Single-Cell Sequencing data

Documentation for package ‘BASiCS’ version 2.21.0

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.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_CalculateERCC	Convert concentration in moles per microlitre to molecule counts
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_PlotVarianceDecomp	Plot variance decomposition results.
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.