Package: flowFP 1.71.0

Herb Holyst

flowFP: Fingerprinting for Flow Cytometry

Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

Authors:Herb Holyst <[email protected]>, Wade Rogers <[email protected]>

flowFP_1.71.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowFP/json (API)

# Install 'flowFP' in R:

install.packages('flowFP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

fs1 - Example FCS flowSet
fs2 - Example FCS flowSet
plate - 96 well plate data.

On BioConductor:flowFP-1.71.0(bioc 3.24)flowFP-1.70.0(bioc 3.23)

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

flowcytometry cellbasedassays clustering visualization

4.72 score 2 packages 11 scripts 4 mentions 23 exports 28 dependencies

Last updated from:4e1e604258. Checks:1 ERROR, 7 NOTE, 2 OK, 4 WARNING. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	155
linux-devel-arm64	NOTE	233
linux-devel-x86_64	NOTE	207
source / vignettes	OK	227
linux-release-arm64	NOTE	197
linux-release-x86_64	NOTE	222
macos-release-arm64	WARNING	116
macos-release-x86_64	WARNING	289
macos-oldrel-arm64	WARNING	142
macos-oldrel-x86_64	WARNING	372
windows-devel	NOTE	160
windows-release	NOTE	147
windows-oldrel	NOTE	152
wasm-release	OK	617

Exports:append binBoundary counts flowFP flowFPModel flowFPPlex hasClasses is.flowFP is.flowFPModel is.flowFPPlex name nFeatures nInstances nRecursions nRecursions<-parameters plot sampleClasses sampleClasses<-sampleNames show summary tags

Dependencies:BH Biobase BiocGenerics biocmake cpp11 cytolib deldir dir.expiry filelock flowCore flowViz generics hexbin IDPmisc interp jpeg KernSmooth lattice latticeExtra MASS matrixStats png RColorBrewer Rcpp RcppEigen Rhdf5lib RProtoBufLib S4Vectors

Fingerprinting for Flow Cytometry

Rendered fromflowFP_HowTo.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Package overview	flowFP-package
Indexing methods for flowFP and flowFPPlex	[,flowFP,character-method [,flowFP,numeric-method [,flowFPPlex,ANY-method [-methods [[,flowFPPlex,ANY-method [[-methods [[<-,flowFPPlex,numeric,ANY,flowFP-method
Methods to append flowFP fingerprints to a flowFPPlex	append,flowFPPlex,flowFP-method append,flowFPPlex,flowFPPlex-method append,flowFPPlex,list-method append-methods
Return bin boundaries for a flowFPModel	binBoundary binBoundary,flowFP-method binBoundary,flowFPModel-method binBoundary-methods
Method for getting fingerprint data.	counts counts,flowFP-method counts,flowFPPlex-method
Fingerprint constructor	flowFP
Fingerprint class description.	flowFP-class
Fingerprint model constructor	flowFPModel
Fingerprint model class description.	flowFPModel-class
Fingerprint collection constructor.	flowFPPlex
Fingerprint collection class description.	flowFPPlex-class
Example FCS flowSet	fs1
Example FCS flowSet	fs2
Returns TRUE if the flowFP has a class factor for its instances	hasClasses hasClasses,flowFP-method hasClasses,flowFPPlex-method hasClasses-methods
Test to see if object is a flowFP	is.flowFP
Test to see if object is a flowFPModel	is.flowFPModel
Test to see if object is a flowFPPlex	is.flowFPPlex
The number of fingerprints in a flowFPPlex	length,flowFPPlex-method length-methods length<-,flowFPPlex,numeric-method
Get Model Name	name name,flowFP-method name,flowFPModel-method name,flowFPPlex-method name-methods
Returns the number of features in an object.	nFeatures nFeatures,flowFP-method nFeatures,flowFPModel-method nFeatures,flowFPPlex-method nFeatures-methods
Returns the number of instances in an object.	nInstances nInstances,flowFP-method nInstances,flowFPPlex-method nInstances-methods
Methods to set or get nRecursions	nRecursions nRecursions,flowFP-method nRecursions,flowFPModel-method nRecursions,flowFPPlex-method nRecursions-methods nRecursions<- nRecursions<-,flowFP,numeric-method nRecursions<-,flowFPModel,numeric-method
Return the parameters considered for fingerprinting	parameters,flowFP-method parameters,flowFPModel-method parameters-methods
96 well plate data.	plate
Methods for visualizing flowFP objects	plot,flowFP,flowFrame-method plot,flowFP,flowSet-method plot,flowFP,missing-method plot,flowFPModel,flowFrame-method plot,flowFPModel,flowSet-method plot,flowFPModel,missing-method plot,flowFPPlex,missing-method plot-methods
Gets/Sets the sample classes for a fingerprint.	sampleClasses sampleClasses,flowFP-method sampleClasses,flowFPPlex-method sampleClasses-methods sampleClasses<- sampleClasses<-,flowFP-method sampleClasses<-,flowFPPlex-method
Methods to return sample names from a flowFP object.	sampleNames sampleNames,flowFP-method sampleNames,flowFPPlex-method sampleNames-methods
Methods to view flowFP objects	show,flowFP-method show,flowFPModel-method show,flowFPPlex-method show-methods
Summerizes a flowFP object.	summary,flowFP-method summary-methods
Returns tags from a flowFP object.	tags tags,flowFP-method tags-methods