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Updated: Jan 11, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
Published on: November 7, 2025
THRAISE: An automated and reproducible web platform for RNA-seq analysis
1Department of Integrative Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, South Korea.
Abstract:
Transcriptome-wide High-throughput RNA-seq Analysis Integrated System is a highly streamlined web platform for RNA-seq analysis that requires no programming expertise. Starting from raw NCBI Sequence Read Archive data, it performs the entire analysis pipeline, which includes quality control, alignment, quantification, differential expression, and functional enrichment using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Reactome, and Gene Set Enrichment Analysis. For datasets with limited replicates (n = 1), an alternative workflow is also provided, based on transcripts per million. With real-time monitoring, interactive visualization, and a user-friendly interface, Transcriptome-wide High-throughput RNA-seq Analysis Integrated System enables accessible and reproducible RNA-seq analysis for all researchers.
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