Docker4Circ

Docker4Circ performs comprehensive analysis of circular RNAs (circRNAs) from RNA-Seq data, enabling prediction, classification and annotation using six public databases, back-splice sequence reconstruction, internal alternative splicing definition, alignment-free quantification, and differential expression analysis.

Key Features:

• Prediction and Characterization: Predicts circRNAs and provides classification and annotation using six public databases.
• Back-Splice Sequence Reconstruction: Reconstructs back-splice junction sequences associated with circRNAs.
• Internal Alternative Splicing Analysis: Defines internal alternative structures within circularizing exons.
• Alignment-Free Quantification: Quantifies circRNAs directly from RNA-Seq reads without requiring read alignment.
• Differential Expression Analysis: Identifies circRNAs with significant expression changes across conditions or samples.

Scientific Applications:

• Human circRNA Studies: Enables analysis of circRNA expression and features in human RNA-Seq datasets.
• Model Organism Research: Supports circRNA analysis in model organisms using RNA-Seq data.
• Gene Regulation and Disease Investigations: Facilitates study of circRNA roles in transcriptional and post-transcriptional gene regulation and their deregulation in disease.
• Reproducible Bioinformatics: Produces analyses compatible with reproducible workflows and aligns with Reproducible Bioinformatics Project (RBP) guidelines.

Methodology:

Prediction and classification use six public databases; the workflow reconstructs back-splice sequences, defines internal alternative splicing within circularizing exons, performs alignment-free quantification from RNA-Seq reads, conducts differential expression analysis, and encapsulates computational tasks within Docker containers for reproducibility.