Introduction | Installation | Example data description | Construction of spectral unmixing matrix | Spectral unmixing | Transformation | Investigation of possible unmixing artifacts | Correction of artifacts | Connecting to other non-flowCore compliant applications | Summary | Session information
Package: flowSpecs 1.27.0
Jakob Theorell
flowSpecs: Tools for processing of high-dimensional cytometry data
This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data.
Authors:
flowSpecs_1.27.0.tar.gz
flowSpecs_1.27.0.zip(r-4.7)flowSpecs_1.27.0.zip(r-4.6)flowSpecs_1.27.0.zip(r-4.5)
flowSpecs_1.27.0.tgz(r-4.6-any)flowSpecs_1.27.0.tgz(r-4.5-any)
flowSpecs_1.27.0.tar.gz(r-4.7-any)flowSpecs_1.27.0.tar.gz(r-4.6-any)
flowSpecs_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowSpecs/json (API)
| # Install 'flowSpecs' in R: |
| install.packages('flowSpecs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jtheorell/flowspecs/issues
Datasets:
- fullPanel - A fully stained spectral cytometry sample
- specMat - Spectral unmixing matrix
- unmixCtrls - Unmixing controls
On BioConductor:flowSpecs-1.27.0(bioc 3.24)flowSpecs-1.26.0(bioc 3.23)
softwarecellbasedassaysdatarepresentationimmunooncologyflowcytometrysinglecellvisualizationnormalizationdataimport
Last updated from:b4c6fc3938. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 183 | ||
| linux-devel-x86_64 | NOTE | 337 | ||
| source / vignettes | OK | 290 | ||
| linux-release-x86_64 | NOTE | 249 | ||
| macos-release-arm64 | NOTE | 121 | ||
| macos-oldrel-arm64 | NOTE | 139 | ||
| windows-devel | NOTE | 143 | ||
| windows-release | NOTE | 148 | ||
| windows-oldrel | NOTE | 148 | ||
| wasm-release | OK | 152 |
Exports:arcTranscorrectUnmixcorrMatCreateflowSet2LongDfoneVsAllPlotpeakNormspecMatCalcspecUnmix
Dependencies:BHBiobaseBiocGenericsbiocmakeBiocParallelclicodetoolscpp11cytolibdir.expiryfarverfilelockflowCoreformatRfutile.loggerfutile.optionsgenericsggplot2gluegtableisobandlabelinglambda.rlatticelifecyclemagrittrmatrixStatsplyrR6RColorBrewerRcppreshape2Rhdf5librlangRProtoBufLibS4VectorsS7scalessnowstringistringrvctrsviridisLitewithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Tools for processing high-dimensional cytometry files | flowSpecs-package flowSpecs |
| Efficient inverse hyperbolic cosine transformation | arcTrans |
| Correct defects in spectral unmixing by compensation | correctUnmix |
| Generate a correction matrix for cytometry data analysis | corrMatCreate |
| Convert a flowSet to one long dataframe with all identifiers as separate #columns. | flowSet2LongDf |
| A fully stained spectral cytometry sample | fullPanel |
| Plotting all variables against a single variable | oneVsAllPlot |
| Normalize batch differences in intensities by aligning peaks | peakNorm |
| Spectral unmixing matrix | specMat |
| Calculating the matrix used for spectral unmixing | specMatCalc |
| Spectral unmixing of cytometry files | specUnmix |
| Unmixing controls | unmixCtrls |
