Analysis of Multiplex Cytometric Bead Assays

Reproducible and automated analysis of multiplex bead assays such as CBA (Morgan et al. 2004; ), LEGENDplex (Yu et al. 2015; ), and MACSPlex (Miltenyi Biotec 2014; Application note: Data acquisition and analysis without the MACSQuant analyzer; < https://www.miltenyibiotec.com/upload/assets/IM0021608.PDF>). The package provides functions for streamlined reading of fcs files, and identification of bead clusters and analyte expression. The package eases the calculation of standard curves and the subsequent calculation of the analyte concentration.


pipeline status coverage report CRAN status DOI

Reproducible and easy analysis and evaluation of LEGENDplex, CBA, and MACSPlex experiments.

The companies behind the above beadplex systems, provide their own software for the analysis of the generated data. However, the strong dependence on manual interaction make the respective solutions labour insensitive and above all not always reproducible.

Installation

From CRAN:

install.packages("beadplexr")

Or the development version from GitLab:

# install.packages("devtools")
devtools::install_git("https://gitlab.com/ustervbo/beadplexr")
#
# Or with vignettes built
# devtools::install_git("https://gitlab.com/ustervbo/beadplexr", build_vignettes = TRUE)

beadplexr depends on the nloptr package. During the installation of nloptr on an Unix/Linux system, the nlopt library should be autimatically downloaded and installed. If this fails, installing the library with

sudo apt-get install libnlopt-dev

should make it possible to complete the installation of beadplexr.

Getting started

library(beadplexr)

The package comes with a comprehensive example in the vignette 'Analysis of LEGENDplex data with beadplexr':

vignette("legendplex-analysis", package = "beadplexr")

Or read the vignette here.

Citing the package

Please cite as:

Stervbo U, Westhoff TH, Babel N (2018). “beadplexr: Reproducible and automated analysis of multiplex bead assays.” PeerJ, 6, e5794. ISSN 2167-8359, doi: 10.7717/peerj.5794

Get the reference BibTex format here.

News

beadplexr version 0.2.0

Minor changes

  • Add BioLegend panel information
    • Human Adipokine Panel* (13-plex)
    • Human Anti-Virus Response Panel (13-plex)
    • Human CD8/NK Panel (13-plex)
    • Human Inflammation Panel (13-plex)
    • Human Metabolic Panel 1 (4-plex)
  • Add citation
  • Fix problem of missing column names after upgrade of tibble to 2.0

beadplexr version 0.1.0

Initial release - clip the flag!

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("beadplexr")

0.2.0 by Ulrik Stervbo, 6 months ago


https://gitlab.com/ustervbo/beadplexr


Report a bug at https://gitlab.com/ustervbo/beadplexr/issues


Browse source code at https://github.com/cran/beadplexr


Authors: Ulrik Stervbo [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports cluster, dplyr, drc, flowCore, fpc, ggplot2, lazyeval, magrittr, mclust, purrr, raster, tibble, tidyr, yaml

Suggests gridExtra, hexbin, igraph, knitr, rmarkdown, stringr, testthat


See at CRAN