flowSpecs

DOI: 10.18129/B9.bioc.flowSpecs    

Tools for processing of high-dimensional cytometry data

Bioconductor version: Release (3.10)

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 ndcn.ox.ac.uk>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews CellBasedAssays, DataRepresentation, FlowCytometry, ImmunoOncology, SingleCell, Software, Visualization
Version 1.0.1
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports ggplot2 (>= 3.1.0), BiocGenerics(>= 0.30.0), BiocParallel(>= 1.18.1), reshape2 (>= 1.4.3), flowCore(>= 1.50.0), zoo (>= 1.8.6), stats (>= 3.6.0), methods (>= 3.6.0)
LinkingTo
Suggests testthat, knitr, rmarkdown, BiocStyle, flowVS, vulcan, DepecheR
SystemRequirements
Enhances
URL
BugReports https://github.com/jtheorell/flowSpecs/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package flowSpecs_1.0.1.tar.gz
Windows Binary flowSpecs_1.0.1.zip
Mac OS X 10.11 (El Capitan) flowSpecs_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/flowSpecs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/flowSpecs
Package Short Url https://bioconductor.org/packages/flowSpecs/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive

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