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PvSTATEM - an R package for automated analysis of serological data

Overview

This package is a simple tool that handles various raw data formats produced in Multiplex Bead Assay (MBA). In short, it reads the unstructured, raw data from, e.g., the Luminex device and outputs normalised and well-structured data, which can be used later in more advanced downstream analysis.

The package includes three main steps for preprocessing the data:

  1. data reading and manipulation
  2. quality control
  3. data normalisation

PvSTATEM package is developed within the project of the same name - PvSTATEM, an international project aiming at malaria elimination and is financially supported by the HORIZON grant HORIZON-WIDERA-2022-ACCESS-07-01.

🟡 Semi-release version

The package is still in a semi-release version, and new functionalities are being added. We plan to finish this stage of development by the end of 2024 by adding summary reports, quality control tools comparing multiple plates, and different normalisation methods.

Installation

The easiest way to install the package is using the CRAN repository:

install.packages("PvSTATEM")
require(PvSTATEM) # load the installed package

Now, you are ready to use the package to read your files!

Please note that since uploading the package to the CRAN repository requires the volunteers’ time to manually run checks on the packages, the package version currently released on CRAN might not be the latest.

The package is under heavy development, with new features being released weekly. Therefore, if you’d like to test the latest package functionalities, we recommend installing it in the development version. It can be done using a simple command install_github available in the devtools library:

require(devtools)
install_github("mini-pw/PvSTATEM")
require(PvSTATEM) # load the installed package

The first command loads the devtools library (you might need to install it first - using the command install_packages("devtools")), and the second one sources the git repository with the code of our package and automatically installs it.

Examples and instructions

The example use of the package and its functionalities can be found in the vignettes. For more detailed documentation, check the package website.

Contributing and issues

As a project in the development phase, we are open to any suggestions, bug reports, and contributions. If you have any ideas or issues, please report them in the Issues section. Our team of developers will address them as soon as possible.