Package: flowBin 1.43.0
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:
flowBin_1.43.0.tar.gz
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flowBin.pdf |flowBin.html✨
flowBin/json (API)
NEWS
| # Install 'flowBin' in R: |
| install.packages('flowBin', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- aml.sample - Multitube AML sample as example data for flowBin
On BioConductor:flowBin-1.41.0(bioc 3.20)flowBin-1.40.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologycellbasedassaysflowcytometry
Last updated 23 days agofrom:6f2acd386d. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:bin.labelsbin.labels<-bin.parsbin.pars<-checkQNormcontrol.tubescontrol.tubes<-eventsInBinsflowBinflowFPBingetBinExprkMeansBinmapBinsKNNmeasure.parsmeasure.pars<-namename<-quantileNormaliseremoveSparseBinsshowtube.settube.set<-
Dependencies:BHBiobaseBiocGenericsclasscpp11cytolibdeldirflowCoreflowFPflowVizhexbinIDPmiscinterpjpegKernSmoothlatticelatticeExtralimmaMASSmatrixStatspngRColorBrewerRcppRcppEigenRhdf5libRProtoBufLibS4Vectorssnowstatmod
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 |