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flowSpecs

This is the development version of flowSpecs; for the stable release version, see flowSpecs.

Tools for processing of high-dimensional cytometry data


Bioconductor version: Development (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 ki.se>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews CellBasedAssays, DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Normalization, SingleCell, Software, Visualization
Version 1.17.0
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
URL
Bug Reports https://github.com/jtheorell/flowSpecs/issues
See More
Suggests testthat, knitr, rmarkdown, BiocStyle, DepecheR
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Build Report Build Report

Package Archives

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

Source Package flowSpecs_1.17.0.tar.gz
Windows Binary
macOS Binary (x86_64) flowSpecs_1.17.0.tgz
macOS Binary (arm64)
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/
Package Downloads Report Download Stats