Overview | Installation | Stable Release | Development Release | Loading the Package and Importing Data | Reviewing and Correcting Histogram Analyses | Histogram presentation | Correcting a Failed Model Fit | Changing Model Components: Debris Model | Local Minima Traps | Annotating Histograms and Excluding Results | Exporting Results | Size Standards | Gating | The Gating Interface | Interpreting the Gate Plot | Applying a Gate | Further Details | References
Package: flowPloidy 1.39.0
Tyler Smith
flowPloidy: Analyze flow cytometer data to determine sample ploidy
Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.
Authors:
flowPloidy_1.39.0.tar.gz
flowPloidy_1.39.0.zip(r-4.7-any)flowPloidy_1.39.0.zip(r-4.6-any)flowPloidy_1.39.0.zip(r-4.5-any)
flowPloidy_1.39.0.tgz(r-4.6-any)flowPloidy_1.39.0.tgz(r-4.5-any)
flowPloidy_1.39.0.tar.gz(r-4.7-any)flowPloidy_1.39.0.tar.gz(r-4.6-any)
flowPloidy_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowPloidy/json (API)
| # Install 'flowPloidy' in R: |
| install.packages('flowPloidy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/plantarum/flowploidy/issues
On BioConductor:flowPloidy-1.39.0(bioc 3.24)flowPloidy-1.38.0(bioc 3.23)
flowcytometryguiregressionvisualizationbioconductorevolutionflow-cytometrypolyploidy
Last updated from:57a344b0af. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 172 | ||
| linux-devel | NOTE | 296 | ||
| source / vignettes | OK | 224 | ||
| linux-release | NOTE | 292 | ||
| macos-release | NOTE | 143 | ||
| macos-oldrel | NOTE | 118 | ||
| windows-devel | NOTE | 111 | ||
| windows-release | NOTE | 151 | ||
| windows-oldrel | NOTE | 146 | ||
| wasm-release | OK | 136 |
Exports:batchFlowHistbrowseFlowHistfhAnalyzefhAnnotationfhArgsfhBinsfhChannelfhCompsfhCountsfhCVfhDebrisfhFailfhFilefhG2fhGatefhHistDatafhInitfhLimitsfhLinearityfhMetadatafhModelfhNamefhNLSfhOptsfhPeaksfhRawfhRCSfhSamplesfhSpecialParamsfhStandardsfhStdPeakfhStdSelectedfhStdSizesfhTrimRawFlowHistpickInitplotFHsetBinsstdPeakstdSelectedstdSizestabulateFlowHistupdateFlowHistviewFlowChannels
Dependencies:abindbackportsbase64encBHBiobaseBiocGenericsbiocmakebitopsbootbroombslibcachemcarcarDatacaToolsclicolorspacecommonmarkcowplotcpp11cytolibDerivdigestdir.expirydoBydplyrevaluatefarverfastmapfilelockflowCorefontawesomeforecastFormulafracdifffsgenericsggplot2gluegtablehighrhtmltoolshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminpack.lmminqamodelrnlmenloptrnnetnumDerivotelpbkrtestpillarpkgconfigpromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasRhdf5librlangrmarkdownRProtoBufLibS4VectorsS7sassscalesshinysourcetoolsSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunxtableyamlzoo
flowPloidy: Getting Started
Last update: 2019-04-01
Started: 2017-03-21
flowPloidy: Flow Cytometry Histograms
Introduction | Histogram Basics | Histogram Analysis | Standards | References
Last update: 2019-03-20
Started: 2017-03-21
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| browseFlowHist | browseFlowHist |
| FlowHist Accessors | fhAccessors fhAnnotation fhArgs fhBins fhChannel fhComps fhCounts fhCV fhDebris fhFail fhFile fhG2 fhGate fhHistData fhInit fhLimits fhLinearity fhModel fhName fhNLS fhOpts fhPeaks fhRaw fhRCS fhSamples fhSpecialParams fhStandards fhStdPeak fhStdSelected fhStdSizes fhTrimRaw |
| fhAnalyze | fhAnalyze |
| Display metadata present in an FCS file | fhMetadata viewFlowChannels |
| Building Flow Histogram Models | addComponents dropComponents fhModels flowModels makeModel setLimits |
| FlowHist | batchFlowHist FlowHist |
| An S4 class to represent internal standard details for 'FlowHist' objects | FlowStandards stdPeak stdSelected stdSizes |
| Gaussian model components | gauss GaussianComponents |
| An S4 class to represent model components | ModelComponent |
| Interactively select model starting values | pickInit |
| Plot histograms for FlowHist objects | plot.FlowHist |
| Plot the raw data for a FlowHist object | plotFH |
| setBins | setBins |
| exportFlowHist | tabulateFlowHist |
| updateFlowHist | updateFlowHist |
