Bayesian Analysis of Single-Cell Sequencing data


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Documentation for package ‘BASiCS’ version 2.18.0

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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.