atena

atena quantifies expression of transposable elements from RNA-seq data through multiple methods including ERVmap, TEtranscripts, and Telescope, with integrated quantification of TEs and gene transcripts.

Key Features:

• Multiple Quantification Methods: Supports ERVmap, TEtranscripts, and Telescope methods for transposable element expression quantification.
• Common Interface: Provides a unified workflow consisting of building a parameter object, calling the quantification function, and obtaining a SummarizedExperiment object as output.
• Integrated Quantification: Enables simultaneous quantification of transposable elements and gene transcripts in a single analysis.

Scientific Applications:

• Transposable Element Expression Analysis: Quantifies transposable element expression levels from RNA-seq data using established computational methods.
• Integrated Transcriptome Analysis: Enables joint analysis of transposable element and gene expression profiles within the same experimental framework.

Methodology:

The tool implements a parameter object-based workflow where users build a parameter object, call a quantification function with this object, and receive output as a SummarizedExperiment container.