| Statistical methods for flow cytometry data analysis | flowStats-package flowStats |
| These methods are copied from flowViz to eliminate its dependency on curv1Filter and curv2Filter | addName,curv1Filter,character-method addName,curv1Filter,logical-method addName,curv2Filter,character-method addName,curv2Filter,logical-method |
| Automated gating of single populations in 2D | autoGate |
| Sample backgating results | BackGating |
| Bin a test data set using bins previously created by probability binning a control dataset | binByRef |
| Probability binning metirc for comparing the probability binned datasets | calcPBChiSquare |
| Pearsons chi-square statistic for comparing the probability binned datasets | calcPearsonChi |
| Class "curv1Filter" | %in%,flowFrame,curv1Filter-method curv1Filter curv1Filter-class show,curv1Filter-method summarizeFilter,multipleFilterResult,curv1Filter-method |
| Class "curv2Filter" | %in%,flowFrame,curv2Filter-method curv2Filter curv2Filter-class show,curv2Filter-method summarizeFilter,multipleFilterResult,curv2Filter-method |
| Parse curv1Filter output | curvPeaks |
| Find most likely separation between positive and negative populations in 1D | density1d |
| convert ellipse from cov/mu to points used to plot priors | ellipse |
| The version of fdPar from fda 2.4.0 because the new API changes the output. (specifically res$fd$coefs) and thus breaks the landmarkreg call. | fdPar |
| Generate a prior specification based on a flowClust model This function generates a prior specification based on a flowClust fit object It can be passed to a second round of flowClust() with usePrior="yes" The prior could be estimated from a single sample, for example, and then used to speed up the convergence for other samples. | flowClust2Prior |
| Creates a singlet polygon gate using the prediction bands from a robust linear model | gate_singlet singletGate |
| Per-channel normalization based on landmark registration | gaussNorm |
| Multi-dimensional normalization of flow cytometry data | gpaSet |
| (Internal use only) Identify features of flow cytometry data using backgating | idFeatures idFeaturesByBackgating |
| Procrustes analysis. Using singular value decomposition (SVD) to determine a linear transformation to align the points in X to the points in a reference matrix Y. | iProcrustes |
| Sample flow cytometry data | ITN |
| Compute and cluster high density regions in 1D | landmarkMatrix |
| Automated gating of elliptical cell populations in 2D. | %in%,flowFrame,lymphFilter-method lymphFilter lymphFilter-class lymphGate |
| Generate a flowClust prior specification | mkPrior mkPrior,list,flowSet,ANY,missing-method mkPrior,list,flowSet,missing,missing-method mkPrior,missing,flowFrame,missing,missing-method mkPrior,missing,flowSet,ANY,missing-method mkPrior,polygonGate,flowFrame,missing,missing-method mkPrior,polygonGate,flowFrame,numeric,matrix-method mkPrior,rectangleGate,flowFrame,missing,missing-method mkPrior,rectangleGate,flowFrame,numeric,matrix-method |
| Class "norm2Filter" | %in%,flowFrame,norm2Filter-method norm2Filter norm2Filter-class show,norm2Filter-method |
| normalize a GatingSet imported with flowWorkspace, using sequential normalization on the manual gates in the GatingHierarchy. | normalize normalize,GatingSet,missing-method normalize,GatingSetInternal,missing-method normalize-methods |
| Normalization quality assessment | normQA |
| Overton-like subtraction of densities. | overton_like |
| Plots the probability bins overlaid with flowFrame data | plotBins |
| Plots a flowClust prior over some data. | plotPrior |
| Probability binning - a metric for evaluating multivariate differences | proBin |
| Automated quad gating | quadrantGate |
| Find most likely separation between positive and negative populations in 1D | %in%,flowFrame,rangeFilter-method oneDGate rangeFilter rangeFilter-class rangeGate |
| Random Generation from a t Mixture Model with Box-Cox Transformation | SimulateMixture |
| Construct a 'flowSet' for use with 'spillover' by matching channel names to compensation control filenames | spillover_match spillover_match,flowSet-method spillover_match,missing-method spillover_match-flowSet |
| Compute a spillover matrix from a 'flowSet', simplified API | spillover_ng spillover_ng,flowSet-method spillover_ng,missing-method spillover_ng-flowSet |
| Compute a spillover matrix from a flowSet | spillover spillover,flowSet-method spillover-flowSet |
| Normalization based on landmark registration | warpSet warpSet.cytoset warpSetGS warpSetNCDF warpSetNCDFLowMem |
