shinyHTGQC

shinyHTGQC performs quality control of extraction-free HTG EdgeSeq sequencing data by assessing positive and negative control gene expression to flag samples as FAIL or ALERT and evaluate technical success.

Key Features:

• HTGQC R package integration: Implements QC measures and algorithms from the HTGQC R package specifically tailored to HTG EdgeSeq data.
• HTG EdgeSeq-specific QC: Provides quality-control measures designed for extraction-free HTG EdgeSeq protocols and raw sequencing outputs.
• Control gene assessment: Evaluates expression levels of provided positive and negative control genes to determine sample technical success and assign FAIL or ALERT statuses.
• Data visualization: Produces visual outputs to assist interpretation of QC results and identification of problematic samples.

Scientific Applications:

• Tumor and tumor microenvironment profiling: QC of HTG EdgeSeq gene expression datasets used to characterize tumors and their microenvironments.
• Gene expression reliability assessment: Ensures data quality prior to interpretation of gene expression patterns in research using HTG EdgeSeq assays.

Methodology:

Assesses sequencing data quality by analyzing expression levels of positive and negative control genes using algorithms from the HTGQC R package and reporting sample statuses (FAIL or ALERT).