qMAP

FUSION is a computational framework designed to overcome challenges in traditional sncRNA sequencing data analysis by first quantifying unique sncRNA species and then aggregating them into their respective parental RNA families. This family-level integration captures the contributions of individual sncRNA species while enhancing statistical power and robustness for differential abundance analysis.
 
 
Citation: Rawal H.C., Chen Q., and Zhou T., FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs. Bioinformatics, 41, btaf526, 2025. doi:10.1093/bioinformatics/btaf526
SPORTS is a pipeline to anotate and quantify small RNAs from RNA-seq data, which is optimized for rRNA- and tRNA-derived small RNAs. In addition, SPORTS can predict potential RNA modification sites using nucleotide mismatch information. SPORTS is precompiled to annotate small RNAs for a wide range of species across bacteria, fungi, plants, and animals.
 
 
Citation: Shi J., et al., SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs. Genomics, Proteomics & Bioinformatics, 16, 144-151, 2018. doi:10.1016/j.gpb.2018.04.004

SPORTS

FUSION

qMAP is a computational tool to identify RNA differential fragmentation, which uncovers “RNA fragmentome” as a novel layer of regulatory information. By quantifying parental RNA fragmentation profile, qMAP advances small RNA studies beyond conventional abundance-based approaches with mechanistic and translational relevance.
 
 
Citation: Rawal H.C., Yu J., Zhang X., Cai C., Chen Q., and Zhou T., qMAP decodes RNA fragmentation dynamics in development and disease. Molecular Systems Biology, 2026. doi:10.1038/s44320-026-00237-2