GeneTEFlow

GeneTEFlow analyzes gene and locus-specific transposable element (TE) expression from RNA-Seq data for integrated studies of gene and TE regulation.

Key Features:

• Reproducibility and platform independence: Uses Nextflow and Docker to provide reproducible execution across diverse computing environments.
• Automated workflow: Implements a fully automated workflow that minimizes manual intervention during data processing.
• Comprehensive analysis of genes and locus-specific transposable elements: Performs simultaneous analysis of gene expression and locus-specific TE expression from RNA-Seq datasets.

Scientific Applications:

• Embryogenesis: Enables investigation of gene and TE expression dynamics during embryogenesis.
• Neurodevelopment: Supports analysis of gene and TE regulation in neurodevelopmental processes.
• Immune function: Facilitates study of gene and TE expression related to immune functions.
• Human disease studies: Aids exploration of how gene and TE expression contribute to human diseases.

Methodology:

The pipeline uses Nextflow to orchestrate workflow execution and Docker containers to encapsulate software dependencies for analyzing gene and locus-specific TE expression from RNA-Seq data.