ArticleBMC genomics2013
Web-based visual analysis for high-throughput genomics.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation.Frontiers in cellular and infection microbiology · 2020Pooled it
- Genomewide Association Study Identifies Copy Number Variants Associated With Warfarin Dose Response and Risk of Venous Thromboembolism in African Americans.Clinical pharmacology and therapeutics · 2023Article
- Modulating the Heat Sensitivity of Prostate Cancer Cell Lines In Vitro: A New Impact for Focal Therapies.Biomedicines · 2020Article
- JBrowse Connect: A server API to connect JBrowse instances and users.PLoS computational biology · 2020Article
- Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era.Current genomics · 2019Review
- The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.Nucleic acids research · 2018Article
- GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline.GigaScience · 2018Article
- Closha: bioinformatics workflow system for the analysis of massive sequencing data.BMC bioinformatics · 2018Article
- MTOR inhibitor-based combination therapies for pancreatic cancer.British journal of cancer · 2018Article
- The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.Nucleic acids research · 2016Article
- Whole Genome Re-Sequencing Identifies a Quantitative Trait Locus Repressing Carbon Reserve Accumulation during Optimal Growth in Chlamydomonas reinhardtii.Scientific reports · 2016Article
- JBrowse: a dynamic web platform for genome visualization and analysis.Genome biology · 2016Article
- VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams.PloS one · 2016Article
- Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines.Cancer medicine · 2015Article
- NCBI BLAST+ integrated into Galaxy.GigaScience · 2015Article
- Article
- Comparative, transcriptome analysis of self-organizing optic tissues.Scientific data · 2015Article
- Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies.BioMed research international · 2015Review
- Article
- Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG.Bioinformatics (Oxford, England) · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
backgroundVisualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues.
resultsWe have created a platform simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy.
conclusionsVisualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments.
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What OpenQuestion holds
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.