Package: flowBin 1.49.0

Kieran ONeill

flowBin: Combining multitube flow cytometry data by binning

Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.

Authors:Kieran O'Neill

flowBin_1.49.0.tar.gz
flowBin_1.49.0.zip(r-4.7)flowBin_1.49.0.zip(r-4.6)flowBin_1.49.0.zip(r-4.5)
flowBin_1.49.0.tgz(r-4.6-any)flowBin_1.49.0.tgz(r-4.5-any)
flowBin_1.49.0.tar.gz(r-4.7-any)flowBin_1.49.0.tar.gz(r-4.6-any)
flowBin_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowBin/json (API)

# Install 'flowBin' in R:

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

Datasets:

aml.sample - Multitube AML sample as example data for flowBin

On BioConductor:flowBin-1.49.0(bioc 3.24)flowBin-1.48.0(bioc 3.23)

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

immunooncology cellbasedassays flowcytometry

3.30 score 2 scripts 22 exports 33 dependencies

Last updated from:16517b9134. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	160
linux-devel-x86_64	NOTE	249
source / vignettes	OK	223
linux-release-x86_64	NOTE	231
macos-release-arm64	NOTE	135
macos-oldrel-arm64	NOTE	99
windows-devel	NOTE	142
windows-release	NOTE	161
windows-oldrel	NOTE	118
wasm-release	OK	151

Exports:bin.labels bin.labels<-bin.pars bin.pars<-checkQNorm control.tubes control.tubes<-eventsInBins flowBin flowFPBin getBinExpr kMeansBin mapBinsKNN measure.pars measure.pars<-name name<-quantileNormalise removeSparseBins show tube.set tube.set<-

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

flowBin

Rendered fromflowBin.Rnwusingutils::Sweave

Last update: 2014-06-26
Started: 2013-12-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Multitube AML sample as example data for flowBin	aml.sample amlsample
A 'FlowSample', but with binning information for each tube	bin.labels bin.labels,BinnedFlowSample-method bin.labels<- bin.labels<-,BinnedFlowSample,list-method BinnedFlowSample BinnedFlowSample-class
Function to check the quantile normalisation of a FlowSample using flowFP	checkQNorm checkQNorm, checkQNorm,FlowSample,FlowSample-method
Count number of events for each tube in each bin	eventsInBins eventsInBins,BinnedFlowSample-method
function to run the entire flowBin pipeline	flowbin-package flowBin
Bin sample using flowFP binning	flowFPBin flowFPBin,FlowSample-method
A class similar to flowSet, but with extra information needed by flowBin	bin.pars bin.pars,FlowSample-method bin.pars<- bin.pars<-,FlowSample,vector-method control.tubes control.tubes,FlowSample-method control.tubes<- control.tubes<-,FlowSample,vector-method FlowSample FlowSample-class measure.pars measure.pars,FlowSample-method measure.pars<- measure.pars<-,FlowSample,list-method name name,FlowSample-method name<- name<-,FlowSample,character-method show,FlowSample-method tube.set tube.set,FlowSample-method tube.set<- tube.set<-,FlowSample,list-method
Calculate the expression of each bin in a BinnedFlowSample in terms of the measurement markers	getBinExpr getBinExpr,BinnedFlowSample-method
Bin sample using K-means binning	kMeansBin kMeansBin,FlowSample-method
Internal function to map bins by KNN	mapBinsKNN mapBinsKNN,FlowSample-method
quantileNormalise normalise binning paramaters across all tubes of a flowSample	quantileNormalise quantileNormalise,FlowSample-method
Remove bins from a BinnedFlowSample with few events in them	removeSparseBins removeSparseBins,BinnedFlowSample-method
Methods to view flowBin objects	show,BinnedFlowExprSet-method show,CVResult-method show-methods