Terzi di Bergamo Lodovico, Guidetti Francesca, Rossi Davide, Bertoni Francesco, Cascione Luciano
Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland.
Bioinformatics Core Unit, Swiss Institute of Bioinformatics, Bellinzona, Switzerland.
GigaByte. 2022 Dec 2;2022:gigabyte74. doi: 10.46471/gigabyte.74. eCollection 2022.
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.
无提取的HTG EdgeSeq方案用于对基因集进行分析并测量其表达。因此，这些方案经常用于表征肿瘤及其微环境。然而，尽管提供了阳性和对照基因，但对于测序运行中每个样本的技术成功评估几乎没有给出指示。我们开发了HTGQC，一个用于HTG EdgeSeq方案质量控制的R包。此外，shinyHTGQC是一个面向没有计算知识的用户的闪亮应用程序，为数据质量控制和可视化提供了一个易于使用的界面。可以对原始测序输出进行质量检查，并根据阳性和阴性对照基因的表达水平将样本标记为FAIL或ALERT。
