beadplexr

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

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

Installation

From CRAN:

install.packages("beadplexr")

Or the development version from GitLab:

# install.packages("remotes")
remotes::install_gitlab("ustervbo/beadplexr")
#
# Or with vignettes built
# install.packages(c("knitr", "rmarkdown", "gridExtra"))
# remotes::install_gitlab("ustervbo/beadplexr", build_vignettes = TRUE)

beadplexr depends on several packages with system requirements. On an Unix/Linux system the libraries can be installed with

sudo apt install \
    libnlopt-dev \
    libfontconfig1-dev \
    libharfbuzz-dev libfribidi-dev \
    libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev

For other systems, please see the documentation of the individual packages:

• nloptr (needs libnlopt-dev)
• systemfonts (needs libfontconfig1-dev)
• textshaping (needs libharfbuzz-dev libfribidi-dev)
• ragg (needs libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev)

Getting started

library(beadplexr)

The package comes with a comprehensive example in the vignette Analysis of LEGENDplex data with beadplexr. There are some license issues with some packages needed to read and work with flow-data, and the functionality is not included in the package. However, the vignette Preparing flow-data for use with with beadplexr comes with a full description and script to make it easier to prepare flow-data for beadplexr.

vignette("legendplex_analysis", package = "beadplexr")
vignette("preparing_flow_data", package = "beadplexr")

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.