ArticleNucleic acids research2013
miRspring: a compact standalone research tool for analyzing miRNA-seq data.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- FragmentFinder-a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA.NAR genomics and bioinformatics · 2026Article
- MicroRNA Databases and Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
- IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.BMC bioinformatics · 2021Article
- Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing.Briefings in bioinformatics · 2021Article
- Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis.Computers in biology and medicine · 2018Article
- Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening.BMC genomics · 2018Article
- A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia.BMC genomics · 2018Article
- Naturally existing isoforms of miR-222 have distinct functions.Nucleic acids research · 2017Article
- QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing.BMC bioinformatics · 2017Article
- isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology.Frontiers in plant science · 2015Article
- iSRAP - a one-touch research tool for rapid profiling of small RNA-seq data.Journal of extracellular vesicles · 2015Article
- Computational Approaches for the Analysis of ncRNA through Deep Sequencing Techniques.Frontiers in bioengineering and biotechnology · 2015Review
- YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.Nucleic acids research · 2015Article
- eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.BMC genomics · 2014Article
- Expression of microRNAs and other small RNAs in prefrontal cortex in schizophrenia, bipolar disorder and depressed subjects.PloS one · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing for microRNA (miRNA) profiling has revealed a vast complexity of miRNA processing variants, but these are difficult to discern for those without bioinformatics expertise and large computing capability. In this article, we present miRNA Sequence Profiling (miRspring) (http://mirspring.victorchang.edu.au), a software solution that creates a small portable research document that visualizes, calculates and reports on the complexities of miRNA processing. We designed an index-compression algorithm that allows the miRspring document to reproduce a complete miRNA sequence data set while retaining a small file size (typically <3 MB). Through analysis of 73 public data sets, we demonstrate miRspring's features in assessing quality parameters, miRNA cluster expression levels and miRNA processing. Additionally, we report on a new class of miRNA variants, which we term seed-isomiRs, identified through the novel visualization tools of the miRspring document. Further investigation identified that ∼30% of human miRBase entries are likely to have a seed-isomiR. We believe that miRspring will be a highly useful research tool that will enhance the analysis of miRNA data sets and thus increase our understanding of miRNA biology.
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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.