ArticleBioinformatics (Oxford, England)2020
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 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.
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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
5 citing papers in PubMed.
- Escherichia coli promotes colorectal cancer metastasis by maintaining enhancer-promoter loops through releasing neutrophil extracellular traps.Nature communications · 2026Article
- BIGapp: A user-friendly genomic tool kit identified quantitative trait loci for creeping rootedness in alfalfa (Medicago sativa L.).The plant genome · 2025Article
- FoxP3 associates with enhancer-promoter loops to regulate TScience immunology · 2022Article
- Molecular and computational approaches to map regulatory elements in 3D chromatin structure.Epigenetics & chromatin · 2021Review
- Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics.Frontiers in bioinformatics · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationVisualization of multiple genomic data generally requires the use of public or commercially hosted browsers. Flexible visualization of chromatin interaction data as genomic features and network components offer informative insights to gene expression. An open source application for visualizing HiC and chromatin conformation-based data as 2D-arcs accompanied by interactive network analyses is valuable.
resultsDNA Rchitect is a new tool created to visualize HiC and chromatin conformation-based contacts at high (Kb) and low (Mb) genomic resolutions. The user can upload their pre-filtered HiC experiment in bedpe format to the DNA Rchitect web app that we have hosted or to a version they themselves have deployed. Using DNA Rchitect, the uploaded data allows the user to visualize different interactions of their sample, perform simple network analyses, while also offering visualization of other genomic data types. The user can then download their results for additional network functionality offered in network based programs such as Cytoscape. AVAILABILITY AND IMPLEMENTATION: DNA Rchitect is freely available both as a web application written primarily in R available at http://shiny.immgen.org/DNARchitect/ and as an open source released under an MIT license at: https://github.com/alosdiallo/DNA_Rchitect.
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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.