Interactive visualization
View article: Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees Open
Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten…
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Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees Open
Evolview is an interactive tree visualization tool designed to help researchers in visualizing phylogenetic trees and in annotating these with additional information. It offers the user with a platform to upload trees in most common tree f…
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GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens Open
Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static “GrapeTree Layout” algorithm that su…
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JBrowse: a dynamic web platform for genome visualization and analysis Open
JBrowse is a mature web application suitable for genome visualization and analysis.
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Microreact: visualizing and sharing data for genomic epidemiology and phylogeography Open
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temp…
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SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples Open
SynergyFinder (https://synergyfinder.fimm.fi) is a free web-application for interactive analysis and visualization of multi-drug combination response data. Since its first release in 2017, SynergyFinder has become a popular tool for multi-…
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pong: fast analysis and visualization of latent clusters in population genetic data Open
Motivation: A series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation …
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Make Interactive Complex Heatmaps in R Open
Summary Heatmap is a powerful visualization method on two-dimensional data to reveal patterns shared by subsets of rows and columns. In this work, we introduce a new R package InteractiveComplexHeatmap that brings interactivity to the wide…
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The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization Open
Background Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation anal…
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Unsupervised Clickstream Clustering for User Behavior Analysis Open
Online services are increasingly dependent on user participation. Whether it's online social networks or crowdsourcing services, understanding user behavior is important yet challenging. In this paper, we build an unsupervised system to ca…
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The State of the Art in Enhancing Trust in Machine Learning Models with the Use of Visualizations Open
Machine learning (ML) models are nowadays used in complex applications in various domains, such as medicine, bioinformatics, and other sciences. Due to their black box nature, however, it may sometimes be hard to understand and trust the r…
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Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling Open
Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.
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StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps Open
Summary The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence of telomere-to-telomere assemblies with multi-megabase repeats requires new visualization strategies. Here, we intr…
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What you see is what you can change: Human-centered machine learning by interactive visualization Open
© . This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/.
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t-viSNE: Interactive Assessment and Interpretation of t-SNE Projections Open
t-Distributed Stochastic Neighbor Embedding (t-SNE) for the visualization of multidimensional data has proven to be a popular approach, with successful applications in a wide range of domains. Despite their usefulness, t-SNE projections ca…
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Single Cell Portal: an interactive home for single-cell genomics data Open
Single-cell omics research has the power to leave a deep impact on modern healthcare. Sharing data widely and freely advances this progress in both the academic and clinical spheres. We developed the Single Cell Portal (SCP) to maximize th…
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iSEE: Interactive SummarizedExperiment Explorer Open
Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. …
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VAPOR: A Visualization Package Tailored to Analyze Simulation Data in Earth System Science Open
Visualization is an essential tool for analysis of data and communication of findings in the sciences, and the Earth System Sciences (ESS) are no exception. However, within ESS, specialized visualization requirements and data models, parti…
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Personal Augmented Reality for Information Visualization on Large Interactive Displays Open
In this work we propose the combination of large interactive displays with personal head-mounted Augmented Reality (AR) for information visualization to facilitate data exploration and analysis. Even though large displays provide more disp…
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IATK: An Immersive Analytics Toolkit Open
International audience
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shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics Open
shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.…
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The State of the Art of Spatial Interfaces for 3D Visualization Open
We survey the state of the art of spatial interfaces for 3D visualization. Interaction techniques are crucial to data visualization processes and the visualization research community has been calling for more research on interaction for ye…
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CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer Open
MicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising diagnostic and prognostic biomarkers for human cancer. In particular, circulating miRNAs that are secreted into circulation exist in remar…
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Beagle Open
"How common is interactive visualization on the web?" "What is the most popular visualization design?" "How prevalent are pie charts really?" These questions intimate the role of interactive visualization in the real (online) world. In thi…
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Cerebro: interactive visualization of scRNA-seq data Open
Despite the growing availability of sophisticated bioinformatic methods for the analysis of single-cell RNA-seq data, few tools exist that allow biologists without extensive bioinformatic expertise to directly visualize and interact with t…
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How Progressive Visualizations Affect Exploratory Analysis Open
The stated goal for visual data exploration is to operate at a rate that matches the pace of human data analysts, but the ever increasing amount of data has led to a fundamental problem: datasets are often too large to process within inter…
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AliTV—interactive visualization of whole genome comparisons Open
Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are imp…
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Comparison of visualization tools for single-cell RNAseq data Open
In the last decade, single cell RNAseq (scRNAseq) datasets have grown in size from a single cell to millions of cells. Due to its high dimensionality, it is not always feasible to visualize scRNAseq data and share it in a scientific report…
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Designing Progressive and Interactive Analytics Processes for High-Dimensional Data Analysis Open
In interactive data analysis processes, the dialogue between the human and the computer is the enabling mechanism that can lead to actionable observations about the phenomena being investigated. It is of paramount importance that this dial…
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Visual exploration of machine learning results using data cube analysis Open
As complex machine learning systems become more widely adopted, it becomes increasingly challenging for users to understand models or interpret the results generated from the models. We present our ongoing work on developing interactive an…