ArticleNucleic acids research2018
SPAR: small RNA-seq portal for analysis of sequencing experiments.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 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
- Human YRNA 4 (HY4) plasma levels are a prognostic indicator of SARS-CoV-2 infection clinical severity.microPublication biology · 2023Article
- CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue.Communications biology · 2022Article
- FILER: a framework for harmonizing and querying large-scale functional genomics knowledge.NAR genomics and bioinformatics · 2022Article
- MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts.BMC bioinformatics · 2022Article
- Integrated Chromatin Accessibility and Transcriptome Landscapes of 5-Fluorouracil-Resistant Colon Cancer Cells.Frontiers in cell and developmental biology · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale.Nucleic acids research · 2021Article
- Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing.Briefings in bioinformatics · 2021Article
- WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data.F1000Research · 2021Article
- Identification and Quantification of Small RNAs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- SEAweb: the small RNA Expression Atlas web application.Nucleic acids research · 2020Article
- Comprehensive MicroRNA Expression Profile of the Mammary Gland in Lactating Dairy Cows With Extremely Different Milk Protein and Fat Percentages.Frontiers in genetics · 2020Article
- DASHR 2.0: integrated database of human small non-coding RNA genes and mature products.Bioinformatics (Oxford, England) · 2019Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The introduction of new high-throughput small RNA sequencing protocols that generate large-scale genomics datasets along with increasing evidence of the significant regulatory roles of small non-coding RNAs (sncRNAs) have highlighted the urgent need for tools to analyze and interpret large amounts of small RNA sequencing data. However, it remains challenging to systematically and comprehensively discover and characterize sncRNA genes and specifically-processed sncRNA products from these datasets. To fill this gap, we present Small RNA-seq Portal for Analysis of sequencing expeRiments (SPAR), a user-friendly web server for interactive processing, analysis, annotation and visualization of small RNA sequencing data. SPAR supports sequencing data generated from various experimental protocols, including smRNA-seq, short total RNA sequencing, microRNA-seq, and single-cell small RNA-seq. Additionally, SPAR includes publicly available reference sncRNA datasets from our DASHR database and from ENCODE across 185 human tissues and cell types to produce highly informative small RNA annotations across all major small RNA types and other features such as co-localization with various genomic features, precursor transcript cleavage patterns, and conservation. SPAR allows the user to compare the input experiment against reference ENCODE/DASHR datasets. SPAR currently supports analyses of human (hg19, hg38) and mouse (mm10) sequencing data. SPAR is freely available at https://www.lisanwanglab.org/SPAR.
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Registered trials
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