juzheng87 / awesome-biological-visualizations

A list of web-based interactive biological data visualizations.

Awesome Biological Visualizations

Interactive visualization of biological data on the web.

Web-based biology-related visualization tools are often scattered across the internet and difficult to discover. They may be found on GitHub, Twitter, or linked from scientific papers. These tools can be very useful to scientists looking to visualize biological data in the context of diseased or healthy humans or model organisms.

Contents

• Cancer
• Genomics
• 3D Genomics
• Metagenomics
• Epigenomics
• Proteomics
• Spatial transcriptomics
• (Non-spatial) Transcriptomics
• Microscopy
• Connectomics
• Metabolomics
• Mass Spectrometry
• Populations
• Medicine

Cancer

• COSMIC Cancer Browser - Browse COSMIC data by tissue type and histology.
• UCSC Xena - Explore functional genomic data sets for correlations between genomic and/or phenotypic variables.
• cBioPortal for Cancer Genomics - Visualization, analysis and download of large-scale cancer genomics data sets.
• iCoMut Beta for FireBrowse - Interactive exploration of mutation rates, mutation signatures, clinical data, gene mutations.
• MAGI - Visualization and collaborative annotation of genomic aberrations.
• ExploSig - Interactive visualization of mutational signatures and clinical data.
• Race, Gender, and Age in TCGA - An interactive visualization of patient gender, race, and age in The Cancer Genome Atlas (TCGA) dataset.
• OASISPRO - Omics analysis tool for clinical phenotype prediction.
• Signal - Mutational signatures extracted from cancer samples and isogenic cell-based experiments.
• Oncoscape - An integrated suite of analysis tools for users to explore hypotheses related to molecular and clinical data.

Genomics

• UCSC Genome Browser - Interactively visualize genomic data.
• Ensembl - A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
• IMP: Integrative Multi-species Prediction - Analyze your experimental results in the functional context of gene-gene networks from multiple organisms.
• PLACNETw - A graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets.
• PhyD3 - A phylogenetic tree viewer.
• Archaeopteryx - Visualization, analysis, and editing of phylogenetic trees.
• GeneMANIA - Helps predict the function of genes and gene sets.
• Mutaframe - Visualize variants of the human genome.
• Coessentiality - A genome-wide almanac of co-essential modules assigns function to uncharacterized genes.
• Gosling - A grammar-based toolkit for scalable and interactive genomics data visualization.

3D Genomics

• HiGlass - A tool for exploring genomic contact matrices and tracks.
• HiPiler - A tool for visually exploring and aggregating reoccurring patterns (like loops, TADs, etc.) in Hi-C maps.
• Delta - An integrative analysis and visualization platform for 3D genome.
• Juicebox - Visualization for Hi-C data.
• TADkit - 3D genome browser and TADbit front-end.

Metagenomics

• Metaviz - Interactive statistical and visual analysis of metagenomic data.
• Malaria Cell Atlas - Explore how genes are expressed across more than 500 individual Plasmodium parasites.

Epigenomics

• Epiviz - Interactive visual analytics for functional genomics data.
• GIVe - Epigenome and genome interaction.
• WashU Epigenome Browser - Displays many sequencing-based data sets across all or part of the genome, on specific gene sets or pathways, and in the context of their metadata.
• Clustergrammer CCLE Explorer - Browse relative mRNA expression data for cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) by tissue of origin using Clustergrammer.
• Peax - Interactive visual pattern exploration in epigenomic data using unsupervised deep representation learning.

Proteomics

• COSMIC-3D - A platform for understanding cancer mutations in the context of 3D protein structure.
• EzMol - Visualisation and image production of protein and nucleic acid structures.
• LiteMol - Visualization of large-scale macromolecular structure data.

Spatial transcriptomics

• Vitessce - Visual integration tool for exploration of spatial single-cell experiment data.
• Brain mRNA Isoform Atlas - Visualize cell type signatures of alternative splicing in postnatal development.
• AlzMap - Spatial transcriptomics in Alzheimer's disease.
• Loom Viewer - Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.
• TissUUmaps - Interactive visualization of large-scale spatial gene expression and tissue morphology data.
• Giotto Viewer - A web-based visualization package for spatial transcriptomic data.

(Non-spatial) Transcriptomics

• cellxgene - An interactive explorer for single-cell transcriptomics data.
• UCSC Cell Browser - An interactive viewer for single-cell expression.
• L1000FWD - Large-scale visualization of drug-induced transcriptomic signatures.
• ASAP - A collaborative portal to analyze single-cell transcriptomics data.
• SCope - A visualization tool for large-scale scRNA-seq datasets.
• Mouse Brain Atlas - Atlas of cell types from the Linnarsson Lab.
• Broad Institute Single Cell Portal - Reducing barriers and accelerating single-cell research.
• Allen Brain Map - Transcriptomics Explorer - Atlas of human and mouse transcriptomic cell types.
• Single Cell VR - Interactive visualization of single-cell data in virtual reality.
• SPRING - A tool for uncovering high-dimensional structure in single-cell gene expression data.
• START - Shiny Transcriptome Analysis Resource Tool allows users to visualize RNA-seq data starting with count data.
• iSEE - The Interactive SummarizedExperiment Explorer.
• TISCH - Tumor Immune Single-cell Hub (TISCH) is a scRNA-seq database focusing on tumor microenvironment.

Gene expression matrices

• EBI Single Cell Expression Atlas - Single cell gene expression across species.
• MORPHEUS - Versatile matrix visualization and analysis software.
• Clustergrammer - Visualize high-dimensional data as interactive hierarchically clustered heatmaps.

Microscopy

• IONpath MIBItracker - Slide and image data.
• Avivator - A lightweight "batteries-included" WebGL viewer for remote imaging data in Bio-Formats Zarr or OME-TIFF format.

Connectomics

• neuroglancer - Tool for visualization of highly detailed maps of neuronal connectivity in the fly brain.
• Allen Mouse Brain Connectivity Atlas - A high-resolution map of neural connections in the mouse brain.
• FlyWire - A human-AI collaboration to map the fly connectome.

Metabolomics

• Metaspace - A platform for metabolite annotation of imaging mass spectrometry data.

Mass Spectrometry

• Cytosplore - Cytosplore is an interactive visual analysis system for the analysis of mass cytometry data.

Populations

• Nextstrain - Real-time tracking of virus evolution.
• Institute for Health Metrics and Evaluation - Visualizations of disease worldwide.
• Lifespans - Visualization of the lifespans of multiple species.
• Life Expectancy - Life expectancies around the world, 1960 to 2009.

Medicine

• Snake Oil Supplements - Scientific evidence for popular health supplements.
• SieveSifter - Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.