Registration Open for Bioc2024 July 24-26


Tools for processing of high-dimensional cytometry data

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

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


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


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews CellBasedAssays, DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Normalization, SingleCell, Software, Visualization
Version 1.18.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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)
System Requirements
Bug Reports
See More
Suggests testthat, knitr, rmarkdown, BiocStyle, DepecheR
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package flowSpecs_1.18.0.tar.gz
Windows Binary
macOS Binary (x86_64) flowSpecs_1.18.0.tgz
macOS Binary (arm64) flowSpecs_1.18.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats