Package: FlowSOM 2.13.0

Sofie Van Gassen

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.

Authors:Sofie Van Gassen [aut, cre], Artuur Couckuyt [aut], Katrien Quintelier [aut], Annelies Emmaneel [aut], Britt Callebaut [aut], Yvan Saeys [aut]

FlowSOM_2.13.0.tar.gz
FlowSOM_2.13.0.zip(r-4.5)FlowSOM_2.13.0.zip(r-4.4)FlowSOM_2.13.0.zip(r-4.3)
FlowSOM_2.13.0.tgz(r-4.4-arm64)FlowSOM_2.13.0.tgz(r-4.4-x86_64)FlowSOM_2.13.0.tgz(r-4.3-arm64)FlowSOM_2.13.0.tgz(r-4.3-x86_64)
FlowSOM_2.13.0.tar.gz(r-4.5-noble)FlowSOM_2.13.0.tar.gz(r-4.4-noble)
FlowSOM_2.13.0.tgz(r-4.4-emscripten)FlowSOM_2.13.0.tgz(r-4.3-emscripten)
FlowSOM.pdf |FlowSOM.html✨
FlowSOM/json (API)
NEWS

# Install 'FlowSOM' in R:
install.packages('FlowSOM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:FlowSOM-2.13.0(bioc 3.20)FlowSOM-2.12.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

78 exports 2.46 score 88 dependencies 9 dependents 177 mentions

Last updated 2 months agofrom:95a62def4d

Exports:%>%AddAnnotationAddBackgroundAddLabelsAddMSTAddNodesAddPiesAddStarsAddStarsPiesAggregateFlowFramesBuildMSTBuildSOMCountGroupsFlowSOMFlowSOM_colorsFlowSOMmaryFlowSOMSubsetFMeasureget_channelsget_markersGetChannelsGetClusterCVsGetClusterMFIsGetClusterPercentagesPositiveGetClustersGetCountsGetCVsGetFeaturesGetFlowJoLabelsGetMarkersGetMetaclusterCVsGetMetaclusterMFIsGetMetaclusterPercentagesPositiveGetMetaclustersGetMFIsGetPercentagesGroupStatsInitialize_KWSPInitialize_PCAManualVectorMetaclusterCVsMetaClusteringmetaClustering_consensusMetaclusterMFIsNClustersNewDataNMetaclustersParseNodeSizePlot2DScattersPlotCentersPlotClusters2DPlotDimRedPlotFileScattersPlotFlowSOMPlotGroupsPlotLabelsPlotManualBarsPlotMarkerPlotNodePlotNumbersPlotOutliersPlotOverview2DPlotPiesPlotSDPlotStarLegendPlotStarsPlotVariablePurityquery_multipleQueryMultipleQueryStarPlotReadInputSaveClustersToFCSSOMTestOutliersUpdateFlowSOMUpdateMetaclustersUpdateNodeSize

Dependencies:abindALLbackportsBHBiobaseBiocGenericsbootbroomcarcarDatacliclustercolorRampscolorspaceConsensusClusterPluscorrplotcowplotcpp11cytolibDerivdoBydplyrfansifarverflowCoregenericsggforceggnewscaleggplot2ggpubrggrepelggsciggsignifgluegridExtragtableigraphisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolyclippolynompurrrquantregR6RColorBrewerRcppRcppEigenRhdf5librlangRProtoBufLibrstatixRtsneS4VectorsscalesSparseMstringistringrsurvivalsystemfontstibbletidyrtidyselecttweenrutf8vctrsviridisLitewithrXML

FlowSOM

Rendered fromFlowSOM.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2022-03-25
Started: 2014-12-03

Readme and manuals

Help Manual

Help pageTopics
AddAnnotationAddAnnotation
AddBackgroundAddBackground
Add a flowFrame to the data variable of the FlowSOM objectAddFlowFrame
AddLabelsAddLabels
AddMSTAddMST
AddNodesAddNodes
AddPiesAddPies
AddScaleAddScale
AddStarsAddStars
AddStarsPiesAddStarsPies
Aggregate multiple FCS files togetherAggregateFlowFrames
AutoMaxNodeSizeAutoMaxNodeSize
BuildMSTBuildMST
Build a self-organizing mapBuildSOM
Calculate differences in cell counts between groupsCountGroups
Calculate distance matrix using a minimal spanning tree neighborhoodDist.MST
Run the FlowSOM algorithmFlowSOM
FlowSOM default colorsFlowSOM_colors
FlowSOMmaryFlowSOMmary
FlowSOMSubsetFlowSOMSubset
F measureFMeasure
get_channelsget_channels
get_markersget_markers
GetChannelsGetChannels
Get CV values for all clustersGetClusterCVs
Get MFI values for all clustersGetClusterMFIs
Get percentage-positive values for all clustersGetClusterPercentagesPositive
Get cluster label for all individual cellsGetClusters
GetCountsGetCounts
Get CV values for all clustersGetCVs
GetFeaturesGetFeatures
Process a FlowJo workspace fileGetFlowJoLabels
GetMarkersGetMarkers
GetMetaclusterCVsGetMetaclusterCVs
GetMetaclusterMFIsGetMetaclusterMFIs
Get percentage-positive values for all metaclustersGetMetaclusterPercentagesPositive
Get metacluster label for all individual cellsGetMetaclusters
Get MFI values for all clustersGetMFIs
GetPercentagesGetPercentages
gg_color_huegg_color_hue
GroupStatsGroupStats
Select k well spread points from XInitialize_KWSP
Create a grid from first 2 PCA componentsInitialize_PCA
Summarize the gating matrix into one vector, only including the cell types of interestManualVector
Assign nearest node to each datapointMapDataToCodes
MetaclusterCVsMetaclusterCVs
MetaClusteringMetaClustering
MetaClusteringmetaClustering_consensus
MetaclusterMFIsMetaclusterMFIs
NClustersNClusters
NewDataNewData
NMetaclustersNMetaclusters
ParseArcsParseArcs
ParseEdgesParseEdges
ParseLayoutParseLayout
ParseNodeSizeParseNodeSize
ParseQueryParseQuery
ParseSD Parses SD in FlowSOM objectParseSD
Plot2DScattersPlot2DScatters
PlotCentersPlotCenters
PlotClusters2DPlotClusters2D
PlotDimRedPlotDimRed
PlotFileScattersPlotFileScatters
PlotFlowSOMPlotFlowSOM
PlotGroupsPlotGroups
PlotLabelsPlotLabels
PlotManualBarsPlotManualBars
PlotMarkerPlotMarker
PlotNode Plot star chartPlotNode
PlotNumbersPlotNumbers
PlotOutliersPlotOutliers
PlotOverview2DPlotOverview2D
PlotPiesPlotPies
PlotSDPlotSD
PlotStarLegendPlotStarLegend
PlotStarsPlotStars
PlotVariablePlotVariable
Print FlowSOM objectprint.FlowSOM
Calculate mean weighted cluster purityPurity
query_multiplequery_multiple
QueryMultipleQueryMultiple
QueryStarPlotQueryStarPlot
Read FCS-files or flowFramesReadInput
Write FlowSOM clustering results to the original FCS filesSaveClustersToFCS
ScaleStarHeightsScaleStarHeights
Build a self-organizing mapSOM
TestOutliersTestOutliers
UpdateFlowSOMUpdateFlowSOM
UpdateMetaclustersUpdateMetaclusters
UpdateNodeSizeUpdateNodeSize