| BASiCS-deprecated | Deprecated 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_DenoisedCounts | Calculates denoised expression expression counts |
| BASiCS_DenoisedRates | Calculates denoised expression rates |
| BASiCS_DetectHVG | Detection method for highly and lowly variable genes |
| BASiCS_DetectHVG_LVG | Detection method for highly and lowly variable genes |
| BASiCS_DetectLVG | Detection method for highly and lowly variable genes |
| BASiCS_D_TestDE | Detection of genes with changes in expression. |
| 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_showFit | Plotting the trend after Bayesian regression |
| BASiCS_showFit-BASiCS_Chain-method | Plotting the trend after Bayesian regression |
| BASiCS_showFit-method | 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 |
| 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) |
| colnames | 'colnames' method for BASiCS_Chain objects |
| colnames-method | 'colnames' 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 |
| 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 | 'plot' method for BASiCS_Chain objects |
| 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 |
| rownames | 'rownames' method for BASiCS_Chain objects |
| rownames-method | 'rownames' method for BASiCS_Chain objects |
| show-method | 'show' method for BASiCS_Chain objects |
| show-method | 'show' method for BASiCS_Summary objects |
| 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 |