flowSpecs
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 ki.se>
citation("flowSpecs")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Normalization, SingleCell, Software, Visualization |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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 |
| Linking To | |
| Enhances | |
| 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 (x86_64) | flowSpecs_1.18.0.zip |
| macOS Binary (x86_64) | flowSpecs_1.18.0.tgz |
| macOS Binary (arm64) | flowSpecs_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/flowSpecs |
| Source Repository (Developer Access) | git clone [email protected]:packages/flowSpecs |
| Bioc Package Browser | https://code.bioconductor.org/browse/flowSpecs/ |
| Package Short Url | https://bioconductor.org/packages/flowSpecs/ |
| Package Downloads Report | Download Stats |