| Function | Description |
| add.parallel.coordinates | Add a parallel coordinates line to an existing plot |
| "addParameter-methods" | Add a column data variable to the data of a FCS object |
| breakpoints.ProbBin | Obtain break points for Probability binning |
| "checkvars-methods" | Checks the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object. |
| "coerce-methods" | Coercing an object class to another class |
| ContourScatterPlot | Image and Contour Bivariate Plot |
| convertS3toS4 | Converts S3 class FCS object to S4 class FCS object |
| createGate | Gating of a FCS object: Making a Gating/Selection index column for subsequent extraction |
| "dim.FCS-methods" | Obtaining the dimensions of the data of an "FCS-class" object |
| "equals-methods" | Checks equality of two "FCS-class" objects |
| extractGatedData | Extract the data of a FCS object using a specified Gating Index |
| extractGateHistory | Extracting the gating information from the history |
| "FCS-class" | Class "FCS" : Flow Cytometry Standard |
| "FCSgate-class" | Class "FCSgate" Flow Cytometry Standard extension to gating |
| "FCSggobi-class" | Class "FCSggobi" : Dynamic Plots |
| "FCSmetadata-class" | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
| "FCSsummary-class" | Class "FCSsummary" Summary object for a "FCS-class" |
| fcs.type | Objects providing parameters for the raw FCS file types |
| FHCRC.HVTNFCS | Fred Hutchinson Cancer Research Center Sequential Gating Procedure proposed by Julie McElrath's Lab |
| "fixvars-methods" | Checks and fixes the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object. |
| "fluors-methods" | Obtaining the Data of Fluorescence Measurements from a FCS object |
| gate.IPC | Interactive gating of an Image Parallel Coordinates Plot |
| "ggobi-methods" | Dynamic Plotting and Viewing the "FCS" object data high-dimensionally |
| ImageParCoord | Image Parallel Coordinates Plot: Joint and marginal |
| KS.flowcytest | Kolmogorov Smirnoff Test 2-sample |
| legend.CSP | Makes a rough legend for the ContourScatterPlot |
| make.grid | Make a matrix of values allocated in a two dimensional grid |
| "metaData-methods" | Extraction of the FCSmetadata-class object from a FCS-class object |
| pairs.CSP | Contour/Hexbin Scatterplot Matrices |
| parallel.coordinates | Parallel coordinates: Plotting each observation across all variables |
| PercentPos.FCS | Calculate the Percent Positive given a percentile |
| pkci2.flowcytest | Testing the difference of upper-tail distributions of two samples |
| "plot-methods" | Graphical representation of an object |
| plot.ProbBin.FCS | Plots a ProbBin.FCS object |
| plotvar.FCS | Making Univariate/Bivariate plots of the column variables of a FCS object |
| "print-methods" | Printing an object |
| ProbBin.FCS | ProbBin.FCS R-object: Probability binning of 2 samples |
| ProbBin.flowcytest | Test the equivalence of two univariate sample distributions by using Probability Binning and plots the probability-binned histograms of the two samples |
| read.FCS | Reading in a raw binary Flow Cytometry Standard (FCS) file |
| rect.box.idx | Superimposes a rectangle on an existing plot given positional indicies |
| ROC.FCS | ROC (Receiver Operating Characteristic) Curve: Percentage Positives for Flow Cytometry data |
| runflowcytests | Tests the equivalence of two univariate sample distributions by using four different methods |
| showgate.FCS | Showing the gate and the datapoints within the gate on a prevous plot |
| "show-methods" | Showing an object |
| "subset2assign-methods" | Replacement and/or Addition of new slot or indexed elements using "[[<-" |
| "subset2-methods" | Extraction of slot information using "[[" |
| "subsetassign-methods" | Replacement and/or Addition of new slot or indexed elements using "[<-" |
| "subset-methods" | Extraction of slot information using "[" |
| "summary-methods" | Summary of object |
| summary.ProbBin.FCS | Chi-Squared/Standard Normal Approximation Summary Statistics for a ProbBin.FCS object |
| VRC.HVTNFCS | Sequential Gating Scheme from Vaccine Research Center (VRC), NIH, Bethesda, MD; Mario Roederer, PhD |
| WLR.flowcytest | Weighted Logrank Test for testing the differences between time-to-event, survival curves |
| xgobi.FCS | XGobi: Dynamic Graphics for Data Analysis on FCS R objects |