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.
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)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")
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.