ampliQueso

ampliQueso analyzes custom AmpliSeq-based RNA sequencing data to quantify targeted gene expression signatures and assess genomic variants from targeted amplicon panels.

Key Features:

• Targeted AmpliSeq RNA Data Analysis: Processes RNA sequencing datasets generated from custom AmpliSeq amplicon panels.
• Gene Expression Signature Evaluation: Quantifies expression signals from predefined transcript targets encoded in targeted RNA panels.
• SNP Detection from Amplicon Reads: Enables interrogation of single-nucleotide polymorphisms (SNPs) when sequencing coverage across targeted regions is sufficient.
• Machine Learning Classification Support: Utilizes count matrices derived from amplicon sequencing to evaluate sample classification and disease-associated transcriptomic signatures.

Scientific Applications:

• Targeted Transcriptomics Analysis: Investigates gene expression signatures using custom AmpliSeq RNA panels.
• Disease Biomarker Identification: Distinguishes disease and healthy samples based on targeted transcriptomic profiles.
• Translational and Clinical Research: Supports development and evaluation of targeted gene expression assays for clinical profiling studies.

Methodology:

ampliQueso analyzes count matrices generated from custom AmpliSeq RNA sequencing panels, evaluates gene-level expression signals and SNP information from targeted amplicon reads, and applies machine-learning classification to assess sample separability based on transcriptomic signatures.