Package: flowPloidy 1.33.0
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_1.33.0.tar.gz
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flowPloidy.pdf |flowPloidy.html✨
flowPloidy/json (API)
NEWS
| # 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-1.33.0(bioc 3.21)flowPloidy-1.32.0(bioc 3.20)
flowcytometryguiregressionvisualizationbioconductorevolutionflow-cytometrypolyploidy
Last updated 4 months agofrom:1117775c89. Checks:5 OK, 2 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-mac | WARNING | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | OK | Jan 28 2025 |
| R-4.4-mac | OK | Jan 28 2025 |
| R-4.3-win | OK | Jan 28 2025 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:batchFlowHistbrowseFlowHistfhAnalyzefhAnnotationfhArgsfhBinsfhChannelfhCompsfhCountsfhCVfhDebrisfhFailfhFilefhG2fhGatefhHistDatafhInitfhLimitsfhLinearityfhModelfhNLSfhOptsfhPeaksfhRawfhRCSfhSamplesfhSpecialParamsfhStandardsfhStdPeakfhStdSelectedfhStdSizesfhTrimRawFlowHistpickInitplotFHsetBinsstdPeakstdSelectedstdSizestabulateFlowHistupdateFlowHistviewFlowChannels
Dependencies:abindbackportsbase64encBHBiobaseBiocGenericsbitopsbootbroombslibcachemcarcarDatacaToolsclicolorspacecommonmarkcowplotcpp11crayoncytolibDerivdigestdoBydplyrevaluatefansifarverfastmapflowCorefontawesomeFormulafsgenericsggplot2gluegtablehighrhtmltoolshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminpack.lmminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasRhdf5librlangrmarkdownRProtoBufLibS4VectorssassscalesshinysourcetoolsSparseMstringistringrsurvivaltibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml
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 fhNLS fhOpts fhPeaks fhRaw fhRCS fhSamples fhSpecialParams fhStandards fhStdPeak fhStdSelected fhStdSizes fhTrimRaw |
| fhAnalyze | fhAnalyze |
| Building Flow Histogram Models | addComponents dropComponents fhModels flowModels makeModel setLimits |
| FlowHist | batchFlowHist FlowHist |
| flowPloidy: A package for analyzing Flow Cytometry Histograms | flowPloidy |
| 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 |
| viewFlowChannels | viewFlowChannels |
