End-to-End Data Automation for Pooled Sample SARS-CoV-2 Using R and Other Open-Source Tools.

Background: Due to supply chain shortages of reagents for real-time (RT)-PCR for SARS-CoV-2 and increasing demand on technical staff, an end-to-end data automation strategy for SARS-CoV-2 sample pooling and singleton analysis became necessary in the summer of 2020.

Methods: Using entirely open source software tools-Linux, bash, R, RShiny, ShinyProxy, and Docker-we developed a modular software application stack to manage the preanalytical, analytical, and postanalytical processes for singleton and pooled testing in a 5-week time frame.

Results: Pooling was operationalized for 81 days, during which time 64 pooled runs were performed for a total of 5320 sample pools and approximately 21 280 patient samples in 4:1 format.

Reproducible manuscript preparation with RMarkdown application to JMSACL and other Elsevier Journals.

Introduction: With the rising complexity of modern multimarker analytical techniques and notable scientific publication retractions required for erroneous statistical analysis, there is increasing awareness of the importance of research transparency and reproducibility. The development of mature open-source tools for literate programming in multiple langauge paradigms has made fully-reproducible authorship possible.

Objectives: We describe the procedure for manuscript preparation using RMarkdown and the R statistical programming language with application to JMSACL or any other Elsevier journal.