DOI: 10.18129/B9.bioc.flowSpecs  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see flowSpecs.

Tools for processing of high-dimensional cytometry data

Bioconductor version: 3.16

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.

Author: Jakob Theorell [aut, cre]

Maintainer: Jakob Theorell <jakob.theorell at ki.se>

Citation (from within R, enter citation("flowSpecs")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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HTML R Script Example workflow for processing of raw spectral cytometry files
PDF   Reference Manual
Text   NEWS


biocViews CellBasedAssays, DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Normalization, SingleCell, Software, Visualization
Version 1.12.0
In Bioconductor since BioC 3.10 (R-3.6) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports ggplot2 (>= 3.1.0), BiocGenerics(>= 0.30.0), BiocParallel(>= 1.18.1), Biobase(>= 2.48.0), reshape2 (>= 1.4.3), flowCore(>= 1.50.0), zoo (>= 1.8.6), stats (>= 3.6.0), methods (>= 3.6.0)
Suggests testthat, knitr, rmarkdown, BiocStyle, DepecheR
BugReports https://github.com/jtheorell/flowSpecs/issues
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Source Package flowSpecs_1.12.0.tar.gz
Windows Binary flowSpecs_1.12.0.zip (64-bit only)
macOS Binary (x86_64) flowSpecs_1.12.0.tgz
macOS Binary (arm64) flowSpecs_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/flowSpecs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/flowSpecs
Bioc Package Browser https://code.bioconductor.org/browse/flowSpecs/
Package Short Url https://bioconductor.org/packages/flowSpecs/
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