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| $.cytoFrame | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| analysePlate | Apply a statistic to the data from each well in a plate |
| as.all | Coercion without introduction of NAs |
| barploterrbar | Barplot with error bars. |
| collectdat | Specialized functions for Dorit Arlt's (DKFZ) proliferation assay project |
| colnames,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| colnames,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| colnames<-,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| colnames<-,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| combineFrames | Combine the cytoFrames within a cytoSet according to some grouping factor |
| csApply | Apply a function over the intensities in a cytoSet |
| cytoFrame-class | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| cytoSet-class | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| ddCt | Apply the ddCt method for a given data set (with or without efficiencies |
| densCols | Scatterplots with smoothed densities color representation |
| description,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| description<-,cytoFrame,character-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| eListWrite | Write the eList |
| estimateCrosstalkPlate | Estimate crosstalk between two color channels. |
| estimateCrosstalkWell | Estimate crosstalk between two color channels. |
| exprs,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| exprs<-,cytoFrame,matrix-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| fitNorm2 | Fit bivariate normal distribution. |
| getDye | Extract the Dye name (CFP or YFP) from the clone ID by pattern matching |
| getElement | Functions to extract atomic data types (numeric, character) and vectors from an XML tree |
| getPradaPar | Set and query global parameters for functions in the prada package |
| getVector | Functions to extract atomic data types (numeric, character) and vectors from an XML tree |
| histStack | Stacked histogram |
| length,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| mapSub2Plate | Map subplate well ID and subplate ID to 96-well plate well ID |
| pData,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| phenoData,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| phenoData<-,cytoSet,phenoData-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| plotNorm2 | Plot fitted bivariate normal distribution. |
| plotPlate | Plot a well statistic in false color representation. |
| readCytoSet | Create a cytoSet object from one or more FCS 3.0 files |
| readFCS | Read an FCS 3.0 file |
| readFCSdata | Auxiliary functions for readFCS |
| readFCSgetPar | Auxiliary functions for readFCS |
| readFCSheader | Auxiliary functions for readFCS |
| readFCStext | Auxiliary functions for readFCS |
| readSDM | Read an SDM file |
| readWellXML | Specialized functions for Dorit Arlt's (DKFZ) proliferation assay project |
| removeCensored | Remove rows that contain censored data |
| removeCensored,cytoFrame-method | Remove rows that contain censored data |
| removeCensored,data.frame-method | Remove rows that contain censored data |
| removeCensored,matrix-method | Remove rows that contain censored data |
| setPradaPars | Set and query global parameters for functions in the prada package |
| shorth | Midpoint of the shorth |
| show,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| show,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| smoothScatter | Scatterplots with smoothed densities color representation |
| splitWellName | Specialized functions for Dorit Arlt's (DKFZ) proliferation assay project |
| statWellLocfit | Calculate a statistic for the data from one well |
| thresholds | Discretize a two-dimensional data space into quadrants by applying thresholds |
| [,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy |
| [,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| [[,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
| [[<-,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |