HTGQC and shinyHTGQC: an R package and shinyR application for quality controls of HTG EDGE-seq protocols

Lodovico Terzi di Bergamo; Francesca Guidetti; Davide Rossi; Francesco Bertoni; Luciano Cascione

doi:10.46471/gigabyte.74

HTGQC and shinyHTGQC: an R package and shinyR application for quality controls of HTG EDGE-seq protocols

GigaByte. 2022 Dec 2:2022:gigabyte74. doi: 10.46471/gigabyte.74. eCollection 2022.

Authors

Lodovico Terzi di Bergamo^{1

2

3}, Francesca Guidetti^{4

5}, Davide Rossi¹, Francesco Bertoni⁴, Luciano Cascione^{2

4}

Affiliations

¹ Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland.
² Bioinformatics Core Unit, Swiss Institute of Bioinformatics, Bellinzona, Switzerland.
³ Department of Health Science and Technology, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland.
⁴ Lymphoma Genomics unit, Institute of Oncology Research, Bellinzona, Switzerland.
⁵ Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.

Abstract

Extraction-free HTG EdgeSeq protocols are used to profile sets of genes and measure their expression. Thus, these protocols are frequently used to characterise tumours and their microenvironments. However, although positive and control genes are provided, little indication is given concerning the assessment of the technical success of each sample within the sequencing run. We developed HTGQC, an R package for the quality control of HTG EdgeSeq protocols. Additionally, shinyHTGQC is a shiny application for users without computing knowledge, providing an easy-to-use interface for data quality control and visualisation. Quality checks can be performed on the raw sequencing outputs, and samples are flagged as FAIL or ALERT based on the expression levels of the positive and negative control genes.

Availability & implementation: The code is freely available at https://github.com/LodovicoTerzi/HTGQC (R package) and https://lodovico.shinyapps.io/shinyHTGQC/ (shiny application), including test datasets.