flowSpecs

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see flowSpecs.

Tools for processing of high-dimensional cytometry data

Bioconductor version: 3.21

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")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("flowSpecs")

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

Documentation

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

browseVignettes("flowSpecs")

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

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Normalization, SingleCell, Software, Visualization

Version 1.22.0

In Bioconductor since BioC 3.10 (R-3.6) (6 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

URL

Bug Reports https://github.com/jtheorell/flowSpecs/issues

Suggests testthat, knitr, rmarkdown, BiocStyle, DepecheR

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