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FlowCytometry

Description Data analysis components.
Child categories
FACSClustering ClusterChooser
FACSPreprocessing
FACSReporting
FACSSummary
Component Version Inputs Outputs Description
AutoGating 1.0 rule, clusters, array filtered, filteredArray, population, populationArray Automatically gate cell populations.
ClusterChooser 1.0 population, plots, sampleAnnotation corrected, fileStatus Graphical tool for cluster population selection.
ClusterFiltering 1.0 fcsDir, in filtered, out Filters columns and/or rows from by clusters using flexible criteria.
CSVListFilter 1.0 clusters, populations filtered, array Filters CSV files in a given folder according to the to extract specific rows given output of AutoGating component.
FCSReader 1.0 in, annotations out, metadata FCSReader imports a FCS file (standards 2.0 and 3.0 supported) and converts it into a tab-delimitted CSV file.
FlowClustModeling 0.1 fcsDir clusters, report Modeling FACS data using flowClust library.
FlowMeans 1.0 inList, in clustersList, clusters, report Clusters rows in CSV files.
GatingSummary 1.0 summaries, sampleAnnotation, panel, population summaryResult, report Generate summay report table and heatmap.
MetaClustering 0.1 optimalClustering metaClusters, metaAssign Meta-Clustering for defining isomorphisms on cells across clusters.
MMClustering 1.0 fcsFiles clusters, postProb, report, mmSpecs, mmParams Normal, t, Skew-normal, and skew-t Mixture-Model Clustering.
OptimalClustering 1.0 clusters, clustStat clusters, report The component takes the output of the MMClustering component, where each data sample has been clustered with multiple different cluster numbers, and determines the optimal cluster number for each sample.
PairWiseClusterPlot 1.0 clusterFiles, clusters, filteredFiles, filtered report Produces pairwise scatter plots from clustered and filtered data.
PlotChannels 1.0 in, fs out Component meant to visualize Flow and Mass Cytometry data before and after transformations.
SamSpectral 1.1 list, in clusters, out SamSPECTRAL clustering of flow cytometry data as described by Zare et al (2010).
Summarise 1.0 clusterFiles, reference summaries Summarises values for different rows of a file (i.e. reference) according to the clustered and possibly filtered result of the file (i.e. clusterFiles).
Transformation 1.0 in out Cell fluorescense intensity transformation for FACS data.

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