.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. |