ArticleBMC bioinformatics2025
UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.
Article in BMC bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
4 citing papers in PubMed.
- Lysosome-related organelles orchestrate guanine crystal formation in pigment cells.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Mapping the transcriptional landscape of algal resistance to viral infection reveals a core expression program.The New phytologist · 2025Article
- Linkage: an interactive web application for linking of DNA regulatory peaks to genes.BMC genomics · 2025Article
- A lung specific escape of intravascular metastatic breast cancer cells from cytotoxic T cell killing.Frontiers in immunology · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe emergence of next-generation sequencing (NGS) marked a revolution in biological research, enabling comprehensive characterization of the transcriptome and detailed analysis of the epigenome landscape. This technology has made it possible to detect differences across cell types, genotypes, and conditions. Advances in short-read sequencing platforms, have produced user-friendly machines that offer high throughput at a reduced cost per base. However, leveraging this data still requires bioinformatics expertise to develop and execute tailored solutions for each specific application. Democratizing access to sequence analysis tools is crucial to empower researchers from diverse fields to harness the full potential of NGS data.
resultsUTAP2, our enhanced version of UTAP published version in 2019 (Kohen et al. in BMC Bioinform 20(1):154, 2019), empowers researchers to unlock the mysteries of gene expression and epigenetic modifications with ease. This user-friendly, open-source pipeline, built by unit programmers and deep sequencing analysts, streamlines transcriptome and epigenome data analysis, handling everything from sequences to gene or peak counts and differentially expressed genes or genomic regions annotation. Results are delivered in organized folders and rich reports packed with plots, tables, and links for effortless interpretation. Since the debut of UTAP, it has been embraced by many researchers at the Weizmann Institute and over 100 citations, thus highlighting its scientific contribution.
conclusionOur User-friendly Transcriptome and Epigenome Analysis Pipeline UTAP2 is available to the broader biomedical research community as an open-source installation. With a single image, it can be installed on both local servers and cloud platforms, allowing users to leverage parallel cluster resources. Once installed UTAP2 enables researchers, even those with limited bioinformatics skills to efficiently, accurately and reliably analyse transcriptome and epigenome sequence data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.