Man pages for catavallejos/BASiCS
Bayesian Analysis of Single-Cell Sequencing data

as.data.frame-methodsConverting BASiCS results objects to data.frames
BASiCS_CalculateERCCConvert concentration in moles per microlitre to molecule...
BASiCS_ChainThe BASiCS_Chain class
BASiCS_Chain-methods'show' method for BASiCS_Chain objects
BASiCS_CorrectOffsetRemove global mean expression offset
BASiCS-defunctDefunct functions in package 'BASiCS'
BASiCS_DenoisedCountsCalculates denoised expression expression counts
BASiCS_DenoisedRatesCalculates denoised expression rates
BASiCS_DetectVGDetection method for highly (HVG) and lowly (LVG) variable...
BASiCS_DiagHistCreate diagnostic plots of MCMC parameters
BASiCS_DiagPlotCreate diagnostic plots of MCMC parameters
BASiCS_DivideAndConquerRun divide and conquer MCMC with BASiCS
BASiCS_DrawGenerate a draw from the posterior of BASiCS using the...
BASiCS_EffectiveSizeCalculate effective sample size for BASiCS_Chain parameters
BASiCS_FilterFilter for input datasets
BASiCS_LoadChainLoads pre-computed MCMC chains generated by the 'BASiCS_MCMC'...
BASiCS_MCMCBASiCS MCMC sampler
BASiCS_MockSCECreate a mock SingleCellExperiment object.
BASiCS_PlotDEProduce plots assessing differential expression results
BASiCS_PlotOffsetVisualise global offset in mean expression between two...
BASiCS_PlotVarianceDecompPlot variance decomposition results.
BASiCS_PlotVGPlots of HVG/LVG search.
BASiCS_PriorParamPrior parameters for BASiCS_MCMC
BASiCS_ResultThe BASiCS_Result class
BASiCS_ResultDEThe BASiCS_ResultDE class
BASiCS_ResultsDEThe BASiCS_ResultsDE class
BASiCS_ResultVGThe BASiCS_ResultVG class
BASiCS_ShowFitPlotting the trend after Bayesian regression
BASiCS_SimGenerates synthetic data according to the model implemented...
BASiCS_SummaryThe BASiCS_Summary class
BASiCS_Summary-methods'show' method for BASiCS_Summary objects
BASiCS_TestDEDetection of genes with changes in expression
BASiCS_VarianceDecompDecomposition of gene expression variability according to...
BASiCS_VarThresholdSearchHVG_LVGDetection method for highly and lowly variable genes using a...
ChainRNAExtract from the chain obtained for the Grun et al (2014)...
ChainRNARegExtract from the chain obtained for the Grun et al (2014)...
ChainSCExtract from the chain obtained for the Grun et al (2014)...
ChainSCRegExtract 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-methodAccessors for the slots of a BASiCS_Chain object
displaySummaryBASiCS-BASiCS_Summary-methodAccessors for the slots of a 'BASiCS_Summary' object
dot-generateSubsetsGenerate balanced subsets for divide and conquer BASiCS
format-methodsMethods for formatting BASiCS_Result and BASiCS_ResultsDE...
makeExampleBASiCS_DataCreate a synthetic SingleCellExperiment example object with...
newBASiCS_ChainCreates a BASiCS_Chain object from pre-computed MCMC chains
newBASiCS_DataCreates 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
rowDatarowData getter and setter for BASiCS_ResultsDE and...
show-BASiCS_ResultDE-methodAccessors for the slots of a 'BASiCS_ResultDE' object
show-BASiCS_ResultsDE-methodAccessors for the slots of a 'BASiCS_ResultsDE' object
show-BASiCS_ResultVG-methodAccessors for the slots of a 'BASiCS_ResultVG' object
subset-BASiCS_Chain-methodA 'subset' method for 'BASiCS_Chain" objects
subset-methodsMethods for subsetting BASiCS_Result and BASiCS_ResultsDE...
Summary-BASiCS_Chain-method'Summary' method for BASiCS_Chain objects
catavallejos/BASiCS documentation built on March 27, 2024, 12:49 a.m.