Browsing by Author "Asimeng, Jesse"

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    Pipeline and tools for the analysis of multiplexed ELISA data
    (Stellenbosch : Stellenbosch University, 2023-03) Asimeng, Jesse; Tromp, Gerard; Maasdorp, Elizna; Gian, van der Spuy; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences. Molecular Biology and Human Genetics.
    ENGLISH ABSTRACT: A cornerstone of scientific progress is independent data verification. It is, therefore, necessary to develop robust analysis pipelines that can ensure reproducible and verifiable analyses. The pipeline should also record all steps and software that generated the results. The analysis of multiplexed ELISA data (Luminex data) can be challenging due to its complexity and variability. In particular, the data preprocessing stage has many steps and is often ad hoc, leading to inconsistency, non-standard approaches and lack of reproducibility. An existing in-house data reprocessing pipeline, the Luminex Pipeline, addresses some of the aforementioned challenges. However, there remains substantial work to extend its utility, robustness, and overall reproducibility. Thus, in this work, I improved the summary statistic reports by using Rmarkdown and implemented unit testing of pipeline components using the R Testthat package. Unit testing ensured the greater robustness of the code, which was compiled into an R package. The pipeline execution was also automated by using the Nextflow workflow management system. Finally, I deployed the pipeline in a Singularity container for execution on any platform including high-performance computing clusters.