Package: flowBeads 1.51.0

Nikolas Pontikos

flowBeads: flowBeads: Analysis of flow bead data

This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.

Authors:Nikolas Pontikos

flowBeads_1.51.0.tar.gz
flowBeads_1.51.0.zip(r-4.7)flowBeads_1.51.0.zip(r-4.6)flowBeads_1.51.0.zip(r-4.5)
flowBeads_1.51.0.tgz(r-4.6-any)flowBeads_1.51.0.tgz(r-4.5-any)
flowBeads_1.51.0.tar.gz(r-4.7-any)flowBeads_1.51.0.tar.gz(r-4.6-any)
flowBeads_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowBeads/json (API)

# Install 'flowBeads' in R:

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

Datasets:

beads1 - Dako beads on day 1
beads2 - Dako beads on day 2
cytocalmef - Cytocal config file
dakomef - Dako config file

On BioConductor:flowBeads-1.51.0(bioc 3.24)flowBeads-1.50.0(bioc 3.23)

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

immunooncology infrastructure flowcytometry cellbasedassays

4.08 score 12 scripts 423 downloads 15 exports 27 dependencies

Last updated from:268fcb0d3b. Checks:1 FAILURE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	FAILURE	158
linux-devel-x86_64	WARNING	248
source / vignettes	OK	216
linux-release-x86_64	WARNING	241
macos-release-arm64	WARNING	144
macos-oldrel-arm64	WARNING	115
windows-devel	WARNING	152
windows-release	WARNING	148
windows-oldrel	WARNING	124
wasm-release	OK	123

Exports:absoluteNormalise BeadFlowFrame gateBeads generateReport getClusteringStats getDate getMEFparams getMEFtransform getParams getTransformFunction hasMEF mefTransform plot relativeNormalise toMEF

Dependencies:BH Biobase BiocGenerics biocmake cpp11 cytolib DEoptimR dir.expiry evaluate filelock flowCore generics highr knitr lattice matrixStats mvtnorm pcaPP Rcpp Rhdf5lib robustbase RProtoBufLib rrcov S4Vectors xfun xtable yaml

Analysis of Flow Cytometry Bead Data

Theory | Loading Bead Files | Gating Bead Data | Relative Normalisation | Generating a Report

Rendered fromHowTo-flowBeads.Rnwusingutils::Sweave

Last update: 2013-06-13
Started: 2013-06-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
flowBeads	flowBeads-package flowBeads
absoluteNormalise	absoluteNormalise absoluteNormalise,GatedBeadFlowFrame,data.frame-method
BeadFlowFrame	BeadFlowFrame BeadFlowFrame-class dBeadFlowFrame
Dako beads on day 1	beads1
Dako beads on day 2	beads2
Cytocal config file	cytocalmef
Dako config file	dakomef
gateBeads	gateBeads gateBeads,BeadFlowFrame-method
GatedBeadFlowFrame	GatedBeadFlowFrame GatedBeadFlowFrame-class
generateReport	generateReport generateReport,GatedBeadFlowFrame,character-method
getClusteringStats	getClusteringStats getClusteringStats,GatedBeadFlowFrame-method
getDate	getDate getDate,flowFrame-method
getMEFparams	getMEFparams getMEFparams,BeadFlowFrame-method
getMEFtransform	getMEFtransform getMEFtransform,GatedBeadFlowFrame-method
getParams	getParams getParams,flowFrame-method
getTransformFunction	getTransformFunction getTransformFunction,BeadFlowFrame-method
hasMEF	hasMEF hasMEF,BeadFlowFrame,character-method
length	length length,flowFrame-method
Logicle transformation constructor	mefTransform
Plot the results of the clustering. Plot only the requested channel which should have a corresponding entry in the MEF files	plot plot,BeadFlowFrame,character-method plot,BeadFlowFrame,missing-method plot,GatedBeadFlowFrame,character-method
relativeNormalise	relativeNormalise relativeNormalise,GatedBeadFlowFrame,GatedBeadFlowFrame-method
BeadFlowFrame	show
toMEF	toMEF toMEF,GatedBeadFlowFrame,flowFrame-method