271 lines
13 KiB
HTML
271 lines
13 KiB
HTML
<h1 id="awesome-biological-visualizations-awesome">Awesome Biological
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Visualizations <a href="https://awesome.re"><img
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src="https://awesome.re/badge.svg" alt="Awesome" /></a></h1>
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<blockquote>
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<p>Interactive visualization of biological data on the web.</p>
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</blockquote>
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<p>Web-based biology-related visualization tools are often scattered
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across the internet and difficult to discover. They may be found on
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GitHub, Twitter, or linked from scientific papers. These tools can be
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very useful to scientists looking to visualize biological data in the
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context of diseased or healthy humans or model organisms.</p>
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<h2 id="contents">Contents</h2>
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<ul>
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<li><a href="#cancer">Cancer</a></li>
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<li><a href="#genomics">Genomics</a></li>
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<li><a href="#3d-genomics">3D Genomics</a></li>
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<li><a href="#metagenomics">Metagenomics</a></li>
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<li><a href="#epigenomics">Epigenomics</a></li>
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<li><a href="#proteomics">Proteomics</a></li>
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<li><a href="#spatial-transcriptomics">Spatial transcriptomics</a></li>
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<li><a href="#non-spatial-transcriptomics">(Non-spatial)
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Transcriptomics</a></li>
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<li><a href="#microscopy">Microscopy</a></li>
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<li><a href="#connectomics">Connectomics</a></li>
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<li><a href="#metabolomics">Metabolomics</a></li>
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<li><a href="#mass-spectrometry">Mass Spectrometry</a></li>
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<li><a href="#populations">Populations</a></li>
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<li><a href="#medicine">Medicine</a></li>
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</ul>
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<h2 id="cancer">Cancer</h2>
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<ul>
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<li><a href="https://cancer.sanger.ac.uk/cosmic/browse/tissue">COSMIC
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Cancer Browser</a> - Browse COSMIC data by tissue type and
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histology.</li>
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<li><a href="https://xenabrowser.net/">UCSC Xena</a> - Explore
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functional genomic data sets for correlations between genomic and/or
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phenotypic variables.</li>
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<li><a href="http://www.cbioportal.org/">cBioPortal for Cancer
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Genomics</a> - Visualization, analysis and download of large-scale
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cancer genomics data sets.</li>
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<li><a href="http://firebrowse.org/iCoMut/">iCoMut Beta for
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FireBrowse</a> - Interactive exploration of mutation rates, mutation
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signatures, clinical data, gene mutations.</li>
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<li><a href="http://magi.brown.edu">MAGI</a> - Visualization and
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collaborative annotation of genomic aberrations.</li>
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<li><a href="http://explosig.lrgr.io">ExploSig</a> - Interactive
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visualization of mutational signatures and clinical data.</li>
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<li><a
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href="https://www.enpicom.com/visual-lab/tcga-visual-exploration-gender-race-age/">Race,
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Gender, and Age in TCGA</a> - An interactive visualization of patient
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gender, race, and age in The Cancer Genome Atlas (TCGA) dataset.</li>
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<li><a href="http://tinyurl.com/oasispro">OASISPRO</a> - Omics analysis
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tool for clinical phenotype prediction.</li>
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<li><a href="https://signal.mutationalsignatures.com/">Signal</a> -
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Mutational signatures extracted from cancer samples and isogenic
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cell-based experiments.</li>
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<li><a href="https://oncoscape.sttrcancer.org/">Oncoscape</a> - An
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integrated suite of analysis tools for users to explore hypotheses
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related to molecular and clinical data.</li>
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</ul>
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<h2 id="genomics">Genomics</h2>
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<ul>
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<li><a href="https://genome.ucsc.edu/">UCSC Genome Browser</a> -
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Interactively visualize genomic data.</li>
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<li><a href="http://www.ensembl.org">Ensembl</a> - A genome browser for
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vertebrate genomes that supports research in comparative genomics,
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evolution, sequence variation and transcriptional regulation.</li>
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<li><a href="http://imp.princeton.edu/">IMP: Integrative Multi-species
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Prediction</a> - Analyze your experimental results in the functional
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context of gene-gene networks from multiple organisms.</li>
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<li><a
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href="https://castillo.dicom.unican.es/ex1/?unique=58f731fec480a">PLACNETw</a>
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- A graph-based tool for reconstruction of plasmids from next generation
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sequence pair-end datasets.</li>
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<li><a
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href="https://phyd3.bits.vib.be/view.php?id=91162629d258a876ee994e9233b2ad87&f=xml">PhyD3</a>
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- A phylogenetic tree viewer.</li>
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<li><a
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href="http://www.phyloxml.org/archaeopteryx-js/bcl2_js.html">Archaeopteryx</a>
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- Visualization, analysis, and editing of phylogenetic trees.</li>
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<li><a href="http://genemania.org/">GeneMANIA</a> - Helps predict the
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function of genes and gene sets.</li>
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<li><a href="http://deogen2.mutaframe.com/">Mutaframe</a> - Visualize
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variants of the human genome.</li>
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<li><a href="http://coessentiality.net">Coessentiality</a> - A
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genome-wide almanac of co-essential modules assigns function to
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uncharacterized genes.</li>
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<li><a href="https://gosling.js.org">Gosling</a> - A grammar-based
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toolkit for scalable and interactive genomics data visualization.</li>
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</ul>
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<h2 id="d-genomics">3D Genomics</h2>
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<ul>
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<li><a href="http://higlass.io/">HiGlass</a> - A tool for exploring
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genomic contact matrices and tracks.</li>
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<li><a href="http://hipiler.higlass.io/">HiPiler</a> - A tool for
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visually exploring and aggregating reoccurring patterns (like loops,
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TADs, etc.) in Hi-C maps.</li>
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<li><a href="http://delta.big.ac.cn/">Delta</a> - An integrative
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analysis and visualization platform for 3D genome.</li>
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<li><a href="http://aidenlab.org/juicebox/">Juicebox</a> - Visualization
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for Hi-C data.</li>
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<li><a
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href="http://sgt.cnag.cat/3dg/tadkit/demo.h/index.html#!/project/dataset?conf=assets%2Fexamples%2Fconf.json">TADkit</a>
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- 3D genome browser and TADbit front-end.</li>
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</ul>
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<h2 id="metagenomics">Metagenomics</h2>
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<ul>
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<li><a href="http://metaviz.cbcb.umd.edu/">Metaviz</a> - Interactive
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statistical and visual analysis of metagenomic data.</li>
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<li><a href="https://www.sanger.ac.uk/science/tools/mca/mca/">Malaria
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Cell Atlas</a> - Explore how genes are expressed across more than 500
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individual Plasmodium parasites.</li>
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</ul>
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<h2 id="epigenomics">Epigenomics</h2>
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<ul>
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<li><a href="http://epiviz.cbcb.umd.edu/4/">Epiviz</a> - Interactive
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visual analytics for functional genomics data.</li>
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<li><a href="https://mcf7.givengine.org/">GIVe</a> - Epigenome and
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genome interaction.</li>
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<li><a href="http://epigenomegateway.wustl.edu/">WashU Epigenome
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Browser</a> - Displays many sequencing-based data sets across all or
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part of the genome, on specific gene sets or pathways, and in the
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context of their metadata.</li>
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<li><a
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href="https://maayanlab.github.io/CCLE_Clustergrammer/">Clustergrammer
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CCLE Explorer</a> - Browse relative mRNA expression data for cancer cell
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lines from the Cancer Cell Line Encyclopedia (CCLE) by tissue of origin
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using Clustergrammer.</li>
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<li><a href="https://github.com/Novartis/peax">Peax</a> - Interactive
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visual pattern exploration in epigenomic data using unsupervised deep
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representation learning.</li>
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</ul>
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<h2 id="proteomics">Proteomics</h2>
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<ul>
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<li><a
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href="https://cancer.sanger.ac.uk/cosmic3d/protein/EGFR">COSMIC-3D</a> -
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A platform for understanding cancer mutations in the context of 3D
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protein structure.</li>
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<li><a href="http://www.sbg.bio.ic.ac.uk/~ezmol/">EzMol</a> -
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Visualisation and image production of protein and nucleic acid
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structures.</li>
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<li><a href="https://webchemdev.ncbr.muni.cz/LiteMol/">LiteMol</a> -
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Visualization of large-scale macromolecular structure data.</li>
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</ul>
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<h2 id="spatial-transcriptomics">Spatial transcriptomics</h2>
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<ul>
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<li><a href="http://vitessce.io">Vitessce</a> - Visual integration tool
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for exploration of spatial single-cell experiment data.</li>
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<li><a href="https://isoformatlas.com/">Brain mRNA Isoform Atlas</a> -
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Visualize cell type signatures of alternative splicing in postnatal
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development.</li>
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<li><a href="https://alzmap.org/">AlzMap</a> - Spatial transcriptomics
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in Alzheimer’s disease.</li>
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<li><a
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href="http://loom.linnarssonlab.org/dataset/cells/osmFISH/osmFISH_SScortex_mouse_all_cells.loom/NrBEoXQGhYDYoAYLRARigZlRgTDpAtAgFhRnSyg0Wrt1rUVuAHYlCYAOD5AzOo3qNmMAJy8ctaeWAYS0jvNoNqotpO6TSioZgmqmLCTJhNt0ebPCpgAWkQA6RJjgkxYxLkwlMrAKxIjr5wbv7~iKxcaLj~0AIkULhK~DAscpwZxGZJ_LIgigB2AK4ANqVKHIbquqi10LVKsgIl5RxyybFQPIGYGAi4yey4PGjDArjsaAgYaBOJaDy4A3i0C4G4EgbUEmiJmIwYmMnm2E0QQA">Loom
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Viewer</a> - Tool for sharing, browsing and visualizing single-cell data
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stored in the Loom file format.</li>
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<li><a href="https://tissuumaps.research.it.uu.se/">TissUUmaps</a> -
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Interactive visualization of large-scale spatial gene expression and
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tissue morphology data.</li>
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<li><a
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href="http://spatialgiotto.rc.fas.harvard.edu/giotto.viewer.html">Giotto
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Viewer</a> - A web-based visualization package for spatial
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transcriptomic data.</li>
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</ul>
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<h2 id="non-spatial-transcriptomics">(Non-spatial) Transcriptomics</h2>
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<ul>
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<li><a
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href="https://www.kidneycellatlas.org/mature-kidney-immune">cellxgene</a>
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- An interactive explorer for single-cell transcriptomics data.</li>
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<li><a href="http://cells.ucsc.edu/?ds=cortex-dev">UCSC Cell Browser</a>
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- An interactive viewer for single-cell expression.</li>
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<li><a href="http://amp.pharm.mssm.edu/L1000FWD/">L1000FWD</a> -
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Large-scale visualization of drug-induced transcriptomic
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signatures.</li>
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<li><a href="https://asap.epfl.ch/">ASAP</a> - A collaborative portal to
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analyze single-cell transcriptomics data.</li>
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<li><a href="http://scope.aertslab.org/">SCope</a> - A visualization
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tool for large-scale scRNA-seq datasets.</li>
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<li><a href="http://mousebrain.org/">Mouse Brain Atlas</a> - Atlas of
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cell types from the Linnarsson Lab.</li>
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<li><a href="https://singlecell.broadinstitute.org/single_cell">Broad
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Institute Single Cell Portal</a> - Reducing barriers and accelerating
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single-cell research.</li>
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<li><a href="http://celltypes.brain-map.org/rnaseq/human_m1_10x">Allen
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Brain Map - Transcriptomics Explorer</a> - Atlas of human and mouse
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transcriptomic cell types.</li>
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<li><a href="https://singlecellvr.herokuapp.com/">Single Cell VR</a> -
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Interactive visualization of single-cell data in virtual reality.</li>
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<li><a
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href="https://kleintools.hms.harvard.edu/tools/springViewer_1_6_dev.html?datasets/mouse_HPCs/basal_bone_marrow/full">SPRING</a>
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- A tool for uncovering high-dimensional structure in single-cell gene
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expression data.</li>
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<li><a href="https://kcvi.shinyapps.io/START/">START</a> - Shiny
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Transcriptome Analysis Resource Tool allows users to visualize RNA-seq
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data starting with count data.</li>
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<li><a href="https://marionilab.cruk.cam.ac.uk/iSEE_allen/">iSEE</a> -
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The Interactive SummarizedExperiment Explorer.</li>
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<li><a href="http://tisch.comp-genomics.org/home/">TISCH</a> - Tumor
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Immune Single-cell Hub (TISCH) is a scRNA-seq database focusing on tumor
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microenvironment.</li>
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</ul>
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<h3 id="gene-expression-matrices">Gene expression matrices</h3>
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<ul>
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<li><a href="https://www.ebi.ac.uk/gxa/sc/home">EBI Single Cell
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Expression Atlas</a> - Single cell gene expression across species.</li>
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<li><a href="https://software.broadinstitute.org/morpheus/">MORPHEUS</a>
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- Versatile matrix visualization and analysis software.</li>
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<li><a href="https://maayanlab.cloud/clustergrammer/">Clustergrammer</a>
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- Visualize high-dimensional data as interactive hierarchically
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clustered heatmaps.</li>
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</ul>
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<h2 id="microscopy">Microscopy</h2>
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<ul>
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<li><a href="https://www.ionpath.com/mibitracker/">IONpath
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MIBItracker</a> - Slide and image data.</li>
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<li><a href="http://avivator.gehlenborglab.org/">Avivator</a> - A
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lightweight “batteries-included” WebGL viewer for remote imaging data in
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Bio-Formats Zarr or OME-TIFF format.</li>
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</ul>
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<h2 id="connectomics">Connectomics</h2>
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<ul>
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<li><a
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href="https://hemibrain-dot-neuroglancer-demo.appspot.com/#!gs://neuroglancer-janelia-flyem-hemibrain/v1.0/neuroglancer_demo_states/kc_apl_mpn1.json">neuroglancer</a>
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- Tool for visualization of highly detailed maps of neuronal
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connectivity in the fly brain.</li>
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<li><a href="http://connectivity.brain-map.org/">Allen Mouse Brain
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Connectivity Atlas</a> - A high-resolution map of neural connections in
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the mouse brain.</li>
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<li><a href="https://flywire.ai/">FlyWire</a> - A human-AI collaboration
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to map the fly connectome.</li>
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</ul>
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<h2 id="metabolomics">Metabolomics</h2>
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<ul>
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<li><a href="https://metaspace2020.eu/">Metaspace</a> - A platform for
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metabolite annotation of imaging mass spectrometry data.</li>
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</ul>
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<h2 id="mass-spectrometry">Mass Spectrometry</h2>
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<ul>
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<li><a href="https://www.cytosplore.org/">Cytosplore</a> - Cytosplore is
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an interactive visual analysis system for the analysis of mass cytometry
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data.</li>
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</ul>
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<h2 id="populations">Populations</h2>
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<ul>
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<li><a href="https://nextstrain.org/">Nextstrain</a> - Real-time
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tracking of virus evolution.</li>
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<li><a
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href="http://www.healthdata.org/results/data-visualizations">Institute
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for Health Metrics and Evaluation</a> - Visualizations of disease
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worldwide.</li>
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<li><a href="http://www.cotrino.com/lifespan/">Lifespans</a> -
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Visualization of the lifespans of multiple species.</li>
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<li><a href="http://projects.flowingdata.com/life-expectancy/">Life
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Expectancy</a> - Life expectancies around the world, 1960 to 2009.</li>
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</ul>
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<h2 id="medicine">Medicine</h2>
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<ul>
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<li><a
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href="http://informationisbeautiful.net/visualizations/snake-oil-scientific-evidence-for-nutritional-supplements-vizsweet/">Snake
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Oil Supplements</a> - Scientific evidence for popular health
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supplements.</li>
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<li><a
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href="http://sieve.fredhutch.org/viz/index.html?study=VTN503&protein=gag&reference=MRK_B_Ad5">SieveSifter</a>
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- Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy
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trials.</li>
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</ul>
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<p><a
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href="https://github.com/keller-mark/awesome-biological-visualizations">biologicalvisualizations.md
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Github</a></p>
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