Man pages for BASiCS
Bayesian Analysis of Single-Cell Sequencing data
| as.data.frame-methods | Converting BASiCS results objects to data.frames |
| BASiCS_Chain | The BASiCS_Chain class |
| BASiCS_Chain-methods | 'show' method for BASiCS_Chain objects |
| BASiCS_CorrectOffset | Remove global mean expression offset |
| BASiCS-defunct | Defunct functions in package 'BASiCS' |
| BASiCS_DenoisedCounts | Calculates denoised expression expression counts |
| BASiCS_DenoisedRates | Calculates denoised expression rates |
| BASiCS_DetectVG | Detection method for highly (HVG) and lowly (LVG) variable... |
| 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... |
| 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'... |
| BASiCS_MCMC | BASiCS MCMC sampler |
| BASiCS_MockSCE | Create a mock SingleCellExperiment object. |
| BASiCS_PlotDE | Produce plots assessing differential expression results |
| BASiCS_PlotOffset | Visualise global offset in mean expression between two... |
| BASiCS_PlotVG | Plots of HVG/LVG search. |
| BASiCS_PriorParam | Prior parameters for BASiCS_MCMC |
| BASiCS_Result | The BASiCS_Result class |
| BASiCS_ResultDE | The BASiCS_ResultDE class |
| BASiCS_ResultsDE | The BASiCS_ResultsDE class |
| BASiCS_ResultVG | The BASiCS_ResultVG class |
| BASiCS_ShowFit | Plotting the trend after Bayesian regression |
| BASiCS_Sim | Generates synthetic data according to the model implemented... |
| 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_VarianceDecomp | Decomposition of gene expression variability according to... |
| BASiCS_VarThresholdSearchHVG_LVG | Detection method for highly and lowly variable genes using a... |
| ChainRNA | Extract from the chain obtained for the Grun et al (2014)... |
| ChainRNAReg | Extract from the chain obtained for the Grun et al (2014)... |
| ChainSC | Extract from the chain obtained for the Grun et al (2014)... |
| ChainSCReg | Extract from the chain obtained for the Grun et al (2014)... |
| dim-BASiCS_Chain-method | 'dim' method for BASiCS_Chain objects |
| dimnames-BASiCS_Chain-method | '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 |
| dot-generateSubsets | Generate balanced subsets for divide and conquer BASiCS |
| format-methods | Methods for formatting BASiCS_Result and BASiCS_ResultsDE... |
| makeExampleBASiCS_Data | Create a synthetic SingleCellExperiment example object with... |
| newBASiCS_Chain | Creates a BASiCS_Chain object from pre-computed MCMC chains |
| newBASiCS_Data | Creates a SingleCellExperiment object from a matrix of... |
| plot-BASiCS_Chain-method | 'plot' method for BASiCS_Chain objects |
| plot-BASiCS_Summary-method | 'plot' method for BASiCS_Summary objects |
| rowData | rowData getter and setter for BASiCS_ResultsDE and... |
| show-BASiCS_ResultDE-method | Accessors for the slots of a 'BASiCS_ResultDE' object |
| show-BASiCS_ResultsDE-method | Accessors for the slots of a 'BASiCS_ResultsDE' object |
| show-BASiCS_ResultVG-method | Accessors for the slots of a 'BASiCS_ResultVG' object |
| subset-BASiCS_Chain-method | A 'subset' method for 'BASiCS_Chain" objects |
| subset-methods | Methods for subsetting BASiCS_Result and BASiCS_ResultsDE... |
| Summary-BASiCS_Chain-method | 'Summary' method for BASiCS_Chain objects |
