Data Visualization and Analytics

MetaTree: an interactive web platform for aligned hierarchical data visualization and multi-group comparison

MetaTree provides an interactive web platform for visualizing and comparing hierarchical quantitative data across groups while preserving topology.

Yomix: An Interactive Tool for the Exploration of Low-Dimensional Embeddings in Omics Data

Yomix is an interactive tool for exploring low-dimensional embeddings in omics data, allowing users to define subsets, compute feature signatures, and compare distributions.

Voronoi tessellation as a complement or replacement for confidence ellipses in the visualization of data projection and clustering results

The paper compares Voronoi tessellation and confidence ellipses for visualizing 2D data projections, finding Voronoi better reveals group overlaps and heterogeneity while confidence ellipses better identify outliers.

phylobar: an R package for multiresolution compositional barplots in omics studies

phylobar provides an R package for interactive multiresolution compositional barplots to visualize hierarchical omics data, enabling exploration across taxonomic resolutions.

nVenn2: faster, simpler generalized quasi-proportional Venn diagrams

nVenn2 generates interpretable quasi-proportional Venn diagrams for large numbers of sets by focusing on non-empty regions, improving efficiency and clarity.

MoMo - Combining Neuron Morphology and Connectivity forInteractive Motif Analysis in Connectomes

MoMo is an interactive visualization framework that analyzes neuron morphology-aware motifs in connectomes, enabling efficient subgraph isomorphism searches and intuitive exploration through a sketch-based interface.

SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data

SEAL integrates spatial imaging context with dimensionality reduction embeddings to improve interpretation of complex datasets through interactive visualization and feature importance analysis.

ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity

ggalign provides a flexible R package for creating composable visualizations of complex, multi-dimensional biological data using layout options and annotation features.

Circuit Mining in Transcriptomics Data

The paper presents a visual analytics tool for identifying target genes in spatial transcriptomics data by analyzing brain circuits.

Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data

Datavzrd creates interactive, portable reports from tabular data without programming, enabling easy sharing and visualization across scientific disciplines.

scatterbar: an R package for visualizing proportional data across spatially resolved coordinates

The paper introduces scatterbar, an R package for visualizing proportional data across spatial coordinates, demonstrating its use on spatial transcriptomics data.

The Art of Brainwaves: A Survey on Event-Related Potential Visualization Practices

This paper surveys ERP visualization practices among M/EEG practitioners, identifies naming inconsistencies, and provides recommendations for improving visualization tools and terminology.

Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit

GenomeSpy is a grammar-based visualization toolkit for genomic data analysis that enables interactive exploration of large datasets, demonstrated on ovarian cancer samples.

langevitour: smooth interactive touring of high dimensions, demonstrated with scRNA-Seq data

langevitour provides interactive animated 2D projections of high-dimensional data using Langevin Dynamics, offering smoother visualization than UMAP for scRNA-Seq data.

Vimo: Visual Analysis of Neuronal Connectivity Motifs

Vimo enables interactive visualization of neuronal connectivity motifs in large brain networks, allowing experts to sketch and analyze motif instances and chains in 3D.

escheR: Unified multi-dimensional visualizations with Gestalt principles

escheR improves 2D data visualization for multi-dimensional data using Gestalt principles, with applications in genomics and spatial transcriptomics.

Dynamic visualization of high-dimensional data

DynamicViz generates dynamic visualizations to assess the reliability of dimensionality reduction methods by quantifying dynamic variability in data.

scatterHatch: an R/Bioconductor package for colorblind accessible visualization of single-cell data

scatterHatch creates accessible scatter plots for single-cell data using color and patterns to improve readability for color-vision deficient readers.

U-CIE : Color encoding of high-dimensional data

U-CIE encodes high-dimensional data as colors using UMAP and CIELAB to preserve structure for visualization.

Hiplot: a comprehensive and easy-to-use web service boosting publication-ready biomedical data visualization

Hiplot provides a web service with 230+ interactive visualization tools for biomedical data, enabling users to generate publication-ready graphics without advanced expertise.

Make Interactive Complex Heatmaps in R

The paper introduces an R package that adds interactivity to static heatmaps, enabling deeper exploration through Shiny web applications.

spiralize: an R Package for Visualizing Data on Spirals

The paper introduces an R package called spiralize for visualizing data on spirals, demonstrating its flexibility and power through real-world examples.

linus: Conveniently explore, share and present large-scale biological trajectory data from a web browser.

linus provides an interactive web-based tool for exploring and sharing large-scale biological trajectory data.

Coral: a web-based visual analysis tool for creating and characterizing cohorts

Coral is a web-based tool for creating and analyzing patient cohorts using genomic and clinical data from multiple sources.

i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results

i2dash creates customizable, interactive web dashboards for visualizing omics data, integrating with R-based analysis pipelines and supporting single-cell RNA-seq workflows.

VICTOR: A visual analytics web application for comparing cluster sets

VICTOR is a web application that compares clustering results using visual analytics tools and multiple metrics.

Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning

PO_SCPLOWEAXC_SCPLOW enables interactive visual pattern search in sequential data using unsupervised deep representation learning, outperforming existing techniques in retrieving similar patterns.

A substrate for modular, extensible data-visualization

The paper introduces a data-visualization framework and Python library to simplify collaboration and visualization of complex datasets across research teams.

BigTop: A Three-Dimensional Virtual Reality Tool for GWAS Visualization

BigTop provides a 3D VR visualization of GWAS data, enhancing interaction and exploration beyond traditional 2D Manhattan plots.

Porthole and Stormcloud: Tools for visualisation of spatiotemporal M/EEG statistics

This paper introduces Porthole and Stormcloud, visualization tools for spatiotemporal M/EEG data, offering enhanced graphical capabilities for print and screen.