ArticleScientific reports2017
UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- A transcriptomic and proteomic map of primary human cell types.Nucleic acids research · 2026Article
- Role of non-coding RNAs in quality improvement of horticultural crops: computational tools, databases, and algorithms for identification and analysis.Functional & integrative genomics · 2025Review
- LncRNAs, RNA Therapeutics, and Emerging Technologies in Liver Pathobiology.Seminars in liver disease · 2025Review
- Comprehensive Transcriptome Analysis Expands lncRNA Functional Profiles in Breast Cancer.International journal of molecular sciences · 2024Article
- Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum.Human mutation · 2022Review
- Article
- A bioinformatic-assisted workflow for genome-wide identification of ncRNAs.NAR genomics and bioinformatics · 2022Article
- ITAS: Integrated Transcript Annotation for Small RNA.Non-coding RNA · 2022Article
- RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.BMC bioinformatics · 2021Article
- Novel lincRNA Discovery and Tissue-Specific Gene Expression across 30 Normal Human Tissues.Genes · 2021Article
- FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.BMC bioinformatics · 2021Article
- Article
- Creation and validation of models to predict response to primary treatment in serous ovarian cancer.Scientific reports · 2021Article
- Article
- Identification of Novel lncRNAs in Ovarian Cancer and Their Impact on Overall Survival.International journal of molecular sciences · 2021Article
- Illuminating lncRNA Function Through Target Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Deregulation of Long Intergenic Non-coding RNAs in CD4+ T Cells of Lamina Propria in Crohn's Disease Through Transcriptome Profiling.Journal of Crohn's & colitis · 2020Article
- Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27.International journal of molecular sciences · 2019Article
- lncRNAs: function and mechanism in cartilage development, degeneration, and regeneration.Stem cell research & therapy · 2019Review
- Ductal Carcinoma in Situ Biomarkers in a Precision Medicine Era: Current and Future Molecular-Based Testing.The American journal of pathology · 2019Review
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long non-coding RNA (lncRNA) is a large class of gene transcripts with regulatory functions discovered in recent years. Many more are expected to be revealed with accumulation of RNA-seq data from diverse types of normal and diseased tissues. However, discovering novel lncRNAs and accurately quantifying known lncRNAs is not trivial from massive RNA-seq data. Herein we describe UClncR, an Ultrafast and Comprehensive lncRNA detection pipeline to tackle the challenge. UClncR takes standard RNA-seq alignment file, performs transcript assembly, predicts lncRNA candidates, quantifies and annotates both known and novel lncRNA candidates, and generates a convenient report for downstream analysis. The pipeline accommodates both un-stranded and stranded RNA-seq so that lncRNAs overlapping with other genes can be predicted and quantified. UClncR is fully parallelized in a cluster environment yet allows users to run samples sequentially without a cluster. The pipeline can process a typical RNA-seq sample in a matter of minutes and complete hundreds of samples in a matter of hours. Analysis of predicted lncRNAs from two test datasets demonstrated UClncR's accuracy and their relevance to sample clinical phenotypes. UClncR would facilitate researchers' novel lncRNA discovery significantly and is publically available at http://bioinformaticstools.mayo.edu/research/UClncR .
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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.