Package: FlowSOM 2.15.0

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]

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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'))

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.

cellbiology flowcytometry clustering visualization software cellbasedassays

6.69 score 10 packages 466 scripts 1.8k downloads 78 exports 89 dependencies

Last updated 23 days agofrom:b617807138. Checks:OK: 2 NOTE: 4 ERROR: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win-x86_64	NOTE	Oct 30 2024
R-4.5-linux-x86_64	NOTE	Oct 30 2024
R-4.4-win-x86_64	NOTE	Oct 30 2024
R-4.4-mac-x86_64	ERROR	Oct 30 2024
R-4.4-mac-aarch64	NOTE	Oct 30 2024
R-4.3-win-x86_64	OK	Oct 30 2024
R-4.3-mac-x86_64	ERROR	Oct 30 2024
R-4.3-mac-aarch64	ERROR	Oct 30 2024

Exports:%>%AddAnnotation AddBackground AddLabels AddMST AddNodes AddPies AddStars AddStarsPies AggregateFlowFrames BuildMST BuildSOM CountGroups FlowSOM FlowSOM_colors FlowSOMmary FlowSOMSubset FMeasure get_channels get_markers GetChannels GetClusterCVs GetClusterMFIs GetClusterPercentagesPositive GetClusters GetCounts GetCVs GetFeatures GetFlowJoLabels GetMarkers GetMetaclusterCVs GetMetaclusterMFIs GetMetaclusterPercentagesPositive GetMetaclusters GetMFIs GetPercentages GroupStats Initialize_KWSP Initialize_PCA ManualVector MetaclusterCVs MetaClustering metaClustering_consensus MetaclusterMFIs NClusters NewData NMetaclusters ParseNodeSize Plot2DScatters PlotCenters PlotClusters2D PlotDimRed PlotFileScatters PlotFlowSOM PlotGroups PlotLabels PlotManualBars PlotMarker PlotNode PlotNumbers PlotOutliers PlotOverview2D PlotPies PlotSD PlotStarLegend PlotStars PlotVariable Purity query_multiple QueryMultiple QueryStarPlot ReadInput SaveClustersToFCS SOM TestOutliers UpdateFlowSOM UpdateMetaclusters UpdateNodeSize

Dependencies:abind ALL backports BH Biobase BiocGenerics boot broom car carData cli cluster colorRamps colorspace ConsensusClusterPlus corrplot cowplot cpp11 cytolib Deriv doBy dplyr fansi farver flowCore Formula generics ggforce ggnewscale ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable igraph isoband labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels matrixStats mgcv microbenchmark minqa modelr munsell nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig polyclip polynom purrr quantreg R6 RColorBrewer Rcpp RcppEigen Rhdf5lib rlang RProtoBufLib rstatix Rtsne S4Vectors scales SparseM stringi stringr survival systemfonts tibble tidyr tidyselect tweenr utf8 vctrs viridisLite withr XML

FlowSOM

Rendered fromFlowSOM.Rnwusingutils::Sweaveon Oct 30 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
AddAnnotation	AddAnnotation
AddBackground	AddBackground
Add a flowFrame to the data variable of the FlowSOM object	AddFlowFrame
AddLabels	AddLabels
AddMST	AddMST
AddNodes	AddNodes
AddPies	AddPies
AddScale	AddScale
AddStars	AddStars
AddStarsPies	AddStarsPies
Aggregate multiple FCS files together	AggregateFlowFrames
AutoMaxNodeSize	AutoMaxNodeSize
BuildMST	BuildMST
Build a self-organizing map	BuildSOM
Calculate differences in cell counts between groups	CountGroups
Calculate distance matrix using a minimal spanning tree neighborhood	Dist.MST
Run the FlowSOM algorithm	FlowSOM
FlowSOM default colors	FlowSOM_colors
FlowSOMmary	FlowSOMmary
FlowSOMSubset	FlowSOMSubset
F measure	FMeasure
get_channels	get_channels
get_markers	get_markers
GetChannels	GetChannels
Get CV values for all clusters	GetClusterCVs
Get MFI values for all clusters	GetClusterMFIs
Get percentage-positive values for all clusters	GetClusterPercentagesPositive
Get cluster label for all individual cells	GetClusters
GetCounts	GetCounts
Get CV values for all clusters	GetCVs
GetFeatures	GetFeatures
Process a FlowJo workspace file	GetFlowJoLabels
GetMarkers	GetMarkers
GetMetaclusterCVs	GetMetaclusterCVs
GetMetaclusterMFIs	GetMetaclusterMFIs
Get percentage-positive values for all metaclusters	GetMetaclusterPercentagesPositive
Get metacluster label for all individual cells	GetMetaclusters
Get MFI values for all clusters	GetMFIs
GetPercentages	GetPercentages
gg_color_hue	gg_color_hue
GroupStats	GroupStats
Select k well spread points from X	Initialize_KWSP
Create a grid from first 2 PCA components	Initialize_PCA
Summarize the gating matrix into one vector, only including the cell types of interest	ManualVector
Assign nearest node to each datapoint	MapDataToCodes
MetaclusterCVs	MetaclusterCVs
MetaClustering	MetaClustering
MetaClustering	metaClustering_consensus
MetaclusterMFIs	MetaclusterMFIs
NClusters	NClusters
NewData	NewData
NMetaclusters	NMetaclusters
ParseArcs	ParseArcs
ParseEdges	ParseEdges
ParseLayout	ParseLayout
ParseNodeSize	ParseNodeSize
ParseQuery	ParseQuery
ParseSD Parses SD in FlowSOM object	ParseSD
Plot2DScatters	Plot2DScatters
PlotCenters	PlotCenters
PlotClusters2D	PlotClusters2D
PlotDimRed	PlotDimRed
PlotFileScatters	PlotFileScatters
PlotFlowSOM	PlotFlowSOM
PlotGroups	PlotGroups
PlotLabels	PlotLabels
PlotManualBars	PlotManualBars
PlotMarker	PlotMarker
PlotNode Plot star chart	PlotNode
PlotNumbers	PlotNumbers
PlotOutliers	PlotOutliers
PlotOverview2D	PlotOverview2D
PlotPies	PlotPies
PlotSD	PlotSD
PlotStarLegend	PlotStarLegend
PlotStars	PlotStars
PlotVariable	PlotVariable
Print FlowSOM object	print.FlowSOM
Calculate mean weighted cluster purity	Purity
query_multiple	query_multiple
QueryMultiple	QueryMultiple
QueryStarPlot	QueryStarPlot
Read FCS-files or flowFrames	ReadInput
Write FlowSOM clustering results to the original FCS files	SaveClustersToFCS
ScaleStarHeights	ScaleStarHeights
Build a self-organizing map	SOM
TestOutliers	TestOutliers
UpdateFlowSOM	UpdateFlowSOM
UpdateMetaclusters	UpdateMetaclusters
UpdateNodeSize	UpdateNodeSize