sRNAtoolbox

sRNAtoolbox performs comprehensive small RNA profiling and differential expression analysis of microRNAs (miRNAs), isomiRs, and other small RNAs from small RNA sequencing data to support normalization, discovery, and comparative studies.

Key Features:

• sRNAbench library protocol support: Processes data from all major RNA library preparation protocols and addresses adapter ligation bias and PCR amplification artifacts.
• sRNAde differential expression: Performs differential expression analysis and detects consensus differential expression across multiple datasets.
• IsomiR and variant profiling: Accommodates miRNA sequence variants (isomiRs) and diverse small RNA molecules in profiling.
• Spike-in integration: Incorporates internal controls such as spike-in sequences for normalization of expression measurements.
• Parallelization: Supports parallel job execution for large-scale analyses.
• Reference database integration: Integrates updated reference databases for annotation and analysis.

Scientific Applications:

• miRNA and small RNA profiling: Quantifies and profiles miRNAs, isomiRs, and other small RNAs from sequencing experiments.
• Differential expression studies: Identifies differentially expressed miRNAs including consensus signals across multiple datasets for comparative analyses.
• Biomarker and clinical research: Supports studies investigating miRNAs as biomarkers or therapeutic targets.
• Repository-scale analyses: Processes large datasets from repositories such as GEO for reproducible analysis of public small RNA-seq data.

Methodology:

Computational processing uses sRNAbench for small RNA-seq data handling with support for multiple library preparation protocols and mitigation of adapter ligation bias and PCR amplification artifacts; sRNAde performs differential expression analysis including consensus detection across datasets, with support for isomiR profiling, spike-in normalization, parallel job execution, and integration of reference databases.