SoloTE

SoloTE quantifies locus-specific transposable element (TE) expression from single-cell RNA-Seq (scRNA-Seq) data to assess TE activity and its potential impact on neighboring gene expression.

Key Features:

• Locus-Specific Expression Analysis: Incorporates the genomic location of TEs to quantify TE activity at specific loci within scRNA-Seq expression matrices.
• Efficient Computational Performance: Optimizes resource usage to process large-scale single-cell datasets with improved computational efficiency.
• Integration with Standard Pipelines: Accepts output files from standard scRNA-Seq processing pipelines to ensure compatibility with existing workflows.

Scientific Applications:

• Characterization of Active TE Repertoires: Identifies transcriptionally active TEs across different cell populations at single-cell resolution.
• Assessing TE Impact on Gene Expression: Predicts potential effects of TE activity on nearby genes based on their genomic context.
• Studying Development, Differentiation, and Disease: Enables analysis of TE expression patterns associated with development, differentiation, and pathogenesis.

Methodology:

Analyzes scRNA-Seq data to identify and quantify TE expression levels at specific genomic loci in individual cells and maps TE-derived signals back to their genomic positions to relate TE activity to nearby genes.