AllelicImbalance

AllelicImbalance detects and quantifies allele-specific expression from RNA-seq reads overlapping heterozygous single-nucleotide polymorphisms to characterize allelic imbalance.

Key Features:

• Detection of Allelic Imbalance: Detects allelic imbalance by examining RNA-seq reads aligned over heterozygous single-nucleotide polymorphisms (SNPs) to identify differential expression between alleles.
• Comprehensive Workflow Management: Integrates quality control, alignment, and allele-specific read counting to manage processing steps and reduce technical biases.
• Bias Detection and Mitigation: Identifies and corrects technical biases arising from sequence differences between alleles to improve reliability of ASE measurements.
• Visualization Capabilities: Visualizes allelic imbalance across genomic regions such as exons to reveal spatial patterns of allele-specific expression.
• ASEset Management Class: Provides the ASEset class to represent and manage allele-specific expression data and associated metadata.

Scientific Applications:

• Genetic Research: Enables identification of genetic variants that influence gene expression by quantifying ASE at heterozygous SNPs.
• Functional Genomics: Supports investigation of transcriptome-level consequences of genetic variation through detection and visualization of allele-specific expression.
• Personalized Medicine: Facilitates identification of allele-specific expression patterns relevant to disease susceptibility or drug response.

Methodology:

Analyzes RNA-seq data aligned over heterozygous SNPs via quality control, alignment to a reference, allele-specific read counting, and identification/correction of technical biases.