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