ArticleBioinformatics (Oxford, England)2015
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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
7 citing papers in PubMed.
- Microbial genomic island discovery, visualization and analysis.Briefings in bioinformatics · 2019Review
- An effective biomedical data migration tool from resource description framework to JSON.Database : the journal of biological databases and curation · 2019Article
- mySyntenyPortal: an application package to construct websites for synteny block analysis.BMC bioinformatics · 2018Article
- IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.Nucleic acids research · 2017Article
- CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.Bioinformatics (Oxford, England) · 2016Article
- Synteny Portal: a web-based application portal for synteny block analysis.Nucleic acids research · 2016Article
- Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationA simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations.
resultsGenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general. AVAILABILITY AND IMPLEMENTATION: GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/. CONTACT: brinkman@sfu.ca.
Indexed as
Identifiers
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.