ArticleRNA (New York, N.Y.)2017
Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench.
Article in RNA (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- "Silicon-On-Insulator"-Based Biosensor for the Detection of MicroRNA Markers of Ovarian Cancer.Micromachines · 2022Article
- The Sum of Two Halves May Be Different from the Whole-Effects of Splitting Sequencing Samples Across Lanes.Genes · 2022Article
- Host Respiratory Transcriptome Signature Associated with Poor Outcome in Children with Influenza-Staphylococcus aureus Pneumonia.The Journal of infectious diseases · 2022Article
- Identification of Two Exosomal miRNAs in Circulating Blood of Cancer Patients by Using Integrative Transcriptome and Network Analysis.Non-coding RNA · 2022Article
- Article
- Identification of alternatively spliced gene isoforms and novel noncoding RNAs by single-molecule long-read sequencing inRNA biology · 2020Article
- RNA-Sequencing Analyses of Small Bacterial RNAs and their Emergence as Virulence Factors in Host-Pathogen Interactions.International journal of molecular sciences · 2020Review
- DNA nanotechnology approaches for microRNA detection and diagnosis.Nucleic acids research · 2019Review
- Visualization of the small RNA transcriptome using seqclusterViz.F1000Research · 2019Article
- RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database.BMC genomics · 2018Article
- The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.Bioinformatics (Oxford, England) · 2018Article
- Oasis 2: improved online analysis of small RNA-seq data.BMC bioinformatics · 2018Article
- microRNAs associated with early neural crest development in Xenopus laevis.BMC genomics · 2018Article
- Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues.PloS one · 2018Article
- miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal.Database : the journal of biological databases and curation · 2018Article
- MicroRNA expression in a phosphaturic mesenchymal tumour.Bone reports · 2017Article
- Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses.BMC genomics · 2017Article
- Article
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6 authors.
Funding
Abstract
Recently, high-throughput sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20 to 25 nt noncoding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA data sets, we present a new interactive pipeline that guides researchers through the various stages of data preprocessing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA data sets. We demonstrate the use of the pipeline on a
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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.