[38;5;12m                                                                       [39m[38;2;255;187;0m[1m[4mAwesome Biological Visualizations [0m[38;5;14m[1m[4m![0m[38;2;255;187;0m[1m[4mAwesome[0m[38;5;14m[1m[4m (https://awesome.re/badge.svg)[0m[38;2;255;187;0m[1m[4m (https://awesome.re)[0m

[38;5;11m[1m▐[0m[38;5;12m [39m[38;5;12mInteractive visualization of biological data on the web.[39m

[38;5;12mWeb-based[39m[38;5;12m [39m[38;5;12mbiology-related[39m[38;5;12m [39m[38;5;12mvisualization[39m[38;5;12m [39m[38;5;12mtools[39m[38;5;12m [39m[38;5;12mare[39m[38;5;12m [39m[38;5;12moften[39m[38;5;12m [39m[38;5;12mscattered[39m[38;5;12m [39m[38;5;12macross[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12minternet[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mdifficult[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12mdiscover.[39m[38;5;12m [39m[38;5;12mThey[39m[38;5;12m [39m[38;5;12mmay[39m[38;5;12m [39m[38;5;12mbe[39m[38;5;12m [39m[38;5;12mfound[39m[38;5;12m [39m[38;5;12mon[39m[38;5;12m [39m[38;5;12mGitHub,[39m[38;5;12m [39m[38;5;12mTwitter,[39m[38;5;12m [39m[38;5;12mor[39m[38;5;12m [39m[38;5;12mlinked[39m[38;5;12m [39m[38;5;12mfrom[39m[38;5;12m [39m[38;5;12mscientific[39m[38;5;12m [39m[38;5;12mpapers.[39m[38;5;12m [39m[38;5;12mThese[39m[38;5;12m [39m[38;5;12mtools[39m[38;5;12m [39m[38;5;12mcan[39m[38;5;12m [39m[38;5;12mbe[39m[38;5;12m [39m[38;5;12mvery[39m[38;5;12m [39m[38;5;12museful[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12mscientists[39m[38;5;12m [39m
[38;5;12mlooking[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12mvisualize[39m[38;5;12m [39m[38;5;12mbiological[39m[38;5;12m [39m[38;5;12mdata[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mcontext[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mdiseased[39m[38;5;12m [39m[38;5;12mor[39m[38;5;12m [39m[38;5;12mhealthy[39m[38;5;12m [39m[38;5;12mhumans[39m[38;5;12m [39m[38;5;12mor[39m[38;5;12m [39m[38;5;12mmodel[39m[38;5;12m [39m[38;5;12morganisms.[39m

[38;2;255;187;0m[4mContents[0m
[38;5;12m- [39m[38;5;14m[1mCancer[0m[38;5;12m (#cancer)[39m
[38;5;12m- [39m[38;5;14m[1mGenomics[0m[38;5;12m (#genomics)[39m
[38;5;12m- [39m[38;5;14m[1m3D Genomics[0m[38;5;12m (#3d-genomics)[39m
[38;5;12m- [39m[38;5;14m[1mMetagenomics[0m[38;5;12m (#metagenomics)[39m
[38;5;12m- [39m[38;5;14m[1mEpigenomics[0m[38;5;12m (#epigenomics)[39m
[38;5;12m- [39m[38;5;14m[1mProteomics[0m[38;5;12m (#proteomics)[39m
[38;5;12m- [39m[38;5;14m[1mSpatial transcriptomics[0m[38;5;12m (#spatial-transcriptomics)[39m
[38;5;12m- [39m[38;5;14m[1m(Non-spatial) Transcriptomics[0m[38;5;12m (#non-spatial-transcriptomics)[39m
[38;5;12m- [39m[38;5;14m[1mMicroscopy[0m[38;5;12m (#microscopy)[39m
[38;5;12m- [39m[38;5;14m[1mConnectomics[0m[38;5;12m (#connectomics)[39m
[38;5;12m- [39m[38;5;14m[1mMetabolomics[0m[38;5;12m (#metabolomics)[39m
[38;5;12m- [39m[38;5;14m[1mMass Spectrometry[0m[38;5;12m (#mass-spectrometry)[39m
[38;5;12m- [39m[38;5;14m[1mPopulations[0m[38;5;12m (#populations)[39m
[38;5;12m- [39m[38;5;14m[1mMedicine[0m[38;5;12m (#medicine)[39m


[38;2;255;187;0m[4mCancer[0m
[38;5;12m- [39m[38;5;14m[1mCOSMIC Cancer Browser[0m[38;5;12m (https://cancer.sanger.ac.uk/cosmic/browse/tissue) - Browse COSMIC data by tissue type and histology.[39m
[38;5;12m- [39m[38;5;14m[1mUCSC Xena[0m[38;5;12m (https://xenabrowser.net/) - Explore functional genomic data sets for correlations between genomic and/or phenotypic variables.[39m
[38;5;12m- [39m[38;5;14m[1mcBioPortal for Cancer Genomics[0m[38;5;12m (http://www.cbioportal.org/) - Visualization, analysis and download of large-scale cancer genomics data sets.[39m
[38;5;12m- [39m[38;5;14m[1miCoMut Beta for FireBrowse[0m[38;5;12m (http://firebrowse.org/iCoMut/) - Interactive exploration of mutation rates, mutation signatures, clinical data, gene mutations.[39m
[38;5;12m- [39m[38;5;14m[1mMAGI[0m[38;5;12m (http://magi.brown.edu) - Visualization and collaborative annotation of genomic aberrations.[39m
[38;5;12m- [39m[38;5;14m[1mExploSig[0m[38;5;12m (http://explosig.lrgr.io) - Interactive visualization of mutational signatures and clinical data.[39m
[38;5;12m- [39m[38;5;14m[1mRace, Gender, and Age in TCGA[0m[38;5;12m (https://www.enpicom.com/visual-lab/tcga-visual-exploration-gender-race-age/) - An interactive visualization of patient gender, race, and age in The Cancer Genome Atlas (TCGA) dataset.[39m
[38;5;12m- [39m[38;5;14m[1mOASISPRO[0m[38;5;12m (http://tinyurl.com/oasispro) - Omics analysis tool for clinical phenotype prediction.[39m
[38;5;12m- [39m[38;5;14m[1mSignal[0m[38;5;12m (https://signal.mutationalsignatures.com/) - Mutational signatures extracted from cancer samples and isogenic cell-based experiments.[39m
[38;5;12m- [39m[38;5;14m[1mOncoscape[0m[38;5;12m (https://oncoscape.sttrcancer.org/) - An integrated suite of analysis tools for users to explore hypotheses related to molecular and clinical data.[39m


[38;2;255;187;0m[4mGenomics[0m
[38;5;12m- [39m[38;5;14m[1mUCSC Genome Browser[0m[38;5;12m (https://genome.ucsc.edu/) - Interactively visualize genomic data.[39m
[38;5;12m- [39m[38;5;14m[1mEnsembl[0m[38;5;12m (http://www.ensembl.org) - A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.[39m
[38;5;12m- [39m[38;5;14m[1mIMP: Integrative Multi-species Prediction[0m[38;5;12m (http://imp.princeton.edu/) - Analyze your experimental results in the functional context of gene-gene networks from multiple organisms.[39m
[38;5;12m- [39m[38;5;14m[1mPLACNETw[0m[38;5;12m (https://castillo.dicom.unican.es/ex1/?unique=58f731fec480a) - A graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets.[39m
[38;5;12m- [39m[38;5;14m[1mPhyD3[0m[38;5;12m (https://phyd3.bits.vib.be/view.php?id=91162629d258a876ee994e9233b2ad87&f=xml) - A phylogenetic tree viewer.[39m
[38;5;12m- [39m[38;5;14m[1mArchaeopteryx[0m[38;5;12m (http://www.phyloxml.org/archaeopteryx-js/bcl2_js.html) - Visualization, analysis, and editing of phylogenetic trees.[39m
[38;5;12m- [39m[38;5;14m[1mGeneMANIA[0m[38;5;12m (http://genemania.org/) - Helps predict the function of genes and gene sets.[39m
[38;5;12m- [39m[38;5;14m[1mMutaframe[0m[38;5;12m (http://deogen2.mutaframe.com/) - Visualize variants of the human genome.[39m
[38;5;12m- [39m[38;5;14m[1mCoessentiality[0m[38;5;12m (http://coessentiality.net) - A genome-wide almanac of co-essential modules assigns function to uncharacterized genes.[39m
[38;5;12m- [39m[38;5;14m[1mGosling[0m[38;5;12m (https://gosling.js.org) - A grammar-based toolkit for scalable and interactive genomics data visualization.[39m

[38;2;255;187;0m[4m3D Genomics[0m
[38;5;12m- [39m[38;5;14m[1mHiGlass[0m[38;5;12m (http://higlass.io/) - A tool for exploring genomic contact matrices and tracks.[39m
[38;5;12m- [39m[38;5;14m[1mHiPiler[0m[38;5;12m (http://hipiler.higlass.io/) - A tool for visually exploring and aggregating reoccurring patterns (like loops, TADs, etc.) in Hi-C maps.[39m
[38;5;12m- [39m[38;5;14m[1mDelta[0m[38;5;12m (http://delta.big.ac.cn/) - An integrative analysis and visualization platform for 3D genome.[39m
[38;5;12m- [39m[38;5;14m[1mJuicebox[0m[38;5;12m (http://aidenlab.org/juicebox/) - Visualization for Hi-C data.[39m
[38;5;12m- [39m[38;5;14m[1mTADkit[0m[38;5;12m (http://sgt.cnag.cat/3dg/tadkit/demo.h/index.html#!/project/dataset?conf=assets%2Fexamples%2Fconf.json) - 3D genome browser and TADbit front-end.[39m

[38;2;255;187;0m[4mMetagenomics[0m
[38;5;12m- [39m[38;5;14m[1mMetaviz[0m[38;5;12m (http://metaviz.cbcb.umd.edu/) - Interactive statistical and visual analysis of metagenomic data.[39m
[38;5;12m- [39m[38;5;14m[1mMalaria Cell Atlas[0m[38;5;12m (https://www.sanger.ac.uk/science/tools/mca/mca/) - Explore how genes are expressed across more than 500 individual Plasmodium parasites.[39m

[38;2;255;187;0m[4mEpigenomics[0m
[38;5;12m- [39m[38;5;14m[1mEpiviz[0m[38;5;12m (http://epiviz.cbcb.umd.edu/4/) - Interactive visual analytics for functional genomics data.[39m
[38;5;12m- [39m[38;5;14m[1mGIVe[0m[38;5;12m (https://mcf7.givengine.org/) - Epigenome and genome interaction.[39m
[38;5;12m- [39m[38;5;14m[1mWashU Epigenome Browser[0m[38;5;12m (http://epigenomegateway.wustl.edu/) - 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.[39m
[38;5;12m- [39m[38;5;14m[1mClustergrammer CCLE Explorer[0m[38;5;12m (https://maayanlab.github.io/CCLE_Clustergrammer/) - Browse relative mRNA expression data for cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) by tissue of origin using Clustergrammer.[39m
[38;5;12m- [39m[38;5;14m[1mPeax[0m[38;5;12m (https://github.com/Novartis/peax) - Interactive visual pattern exploration in epigenomic data using unsupervised deep representation learning.[39m

[38;2;255;187;0m[4mProteomics[0m
[38;5;12m- [39m[38;5;14m[1mCOSMIC-3D[0m[38;5;12m (https://cancer.sanger.ac.uk/cosmic3d/protein/EGFR) - A platform for understanding cancer mutations in the context of 3D protein structure.[39m
[38;5;12m- [39m[38;5;14m[1mEzMol[0m[38;5;12m (http://www.sbg.bio.ic.ac.uk/~ezmol/) - Visualisation and image production of protein and nucleic acid structures.[39m
[38;5;12m- [39m[38;5;14m[1mLiteMol[0m[38;5;12m (https://webchemdev.ncbr.muni.cz/LiteMol/) - Visualization of large-scale [39m
[38;5;12mmacromolecular structure data.[39m


[38;2;255;187;0m[4mSpatial transcriptomics[0m
[38;5;12m- [39m[38;5;14m[1mVitessce[0m[38;5;12m (http://vitessce.io) - Visual integration tool for exploration of spatial single-cell experiment data.[39m
[38;5;12m- [39m[38;5;14m[1mBrain mRNA Isoform Atlas[0m[38;5;12m (https://isoformatlas.com/) - Visualize cell type signatures of alternative splicing in postnatal development.[39m
[38;5;12m- [39m[38;5;14m[1mAlzMap[0m[38;5;12m (https://alzmap.org/) - Spatial transcriptomics in Alzheimer's disease.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mLoom[0m[38;5;14m[1m [0m[38;5;14m[1mViewer[0m[38;5;12m [39m
[38;5;12m(http://loom.linnarssonlab.org/dataset/cells/osmFISH/osmFISH_SScortex_mouse_all_cells.loom/NrBEoXQGhYDYoAYLRARigZlRgTDpAtAgFhRnSyg0Wrt1rUVuAHYlCYAOD5AzOo3qNmMAJy8ctaeWAYS0jvNoNqotpO6TSioZgmqmLCTJhNt0ebPCpgAWkQA6RJjgkxYxLkwlMrAKxIjr5wbv7[39m
[38;5;12m~iKxcaLj~0AIkULhK~DAscpwZxGZJ_LIgigB2AK4ANqVKHIbquqi10LVKsgIl5RxyybFQPIGYGAi4yey4PGjDArjsaAgYaBOJaDy4A3i0C4G4EgbUEmiJmIwYmMnm2E0QQA)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mTool[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12msharing,[39m[38;5;12m [39m[38;5;12mbrowsing[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mvisualizing[39m[38;5;12m [39m[38;5;12msingle-cell[39m[38;5;12m [39m[38;5;12mdata[39m[38;5;12m [39m[38;5;12mstored[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mLoom[39m[38;5;12m [39m[38;5;12mfile[39m[38;5;12m [39m[38;5;12mformat.[39m
[38;5;12m- [39m[38;5;14m[1mTissUUmaps[0m[38;5;12m (https://tissuumaps.research.it.uu.se/) - Interactive visualization of large-scale spatial gene expression and tissue morphology data.[39m
[38;5;12m- [39m[38;5;14m[1mGiotto Viewer[0m[38;5;12m (http://spatialgiotto.rc.fas.harvard.edu/giotto.viewer.html) - A web-based visualization package for spatial transcriptomic data.[39m


[38;2;255;187;0m[4m(Non-spatial) Transcriptomics[0m
[38;5;12m- [39m[38;5;14m[1mcellxgene[0m[38;5;12m (https://www.kidneycellatlas.org/mature-kidney-immune) - An interactive explorer for single-cell transcriptomics data.[39m
[38;5;12m- [39m[38;5;14m[1mUCSC Cell Browser[0m[38;5;12m (http://cells.ucsc.edu/?ds=cortex-dev) - An interactive viewer for single-cell expression.[39m
[38;5;12m- [39m[38;5;14m[1mL1000FWD[0m[38;5;12m (http://amp.pharm.mssm.edu/L1000FWD/) - Large-scale visualization of drug-induced transcriptomic signatures.[39m
[38;5;12m- [39m[38;5;14m[1mASAP[0m[38;5;12m (https://asap.epfl.ch/) - A collaborative portal to analyze single-cell transcriptomics data.[39m
[38;5;12m- [39m[38;5;14m[1mSCope[0m[38;5;12m (http://scope.aertslab.org/) - A visualization tool for large-scale scRNA-seq datasets.[39m
[38;5;12m- [39m[38;5;14m[1mMouse Brain Atlas[0m[38;5;12m (http://mousebrain.org/) - Atlas of cell types from the Linnarsson Lab.[39m
[38;5;12m- [39m[38;5;14m[1mBroad Institute Single Cell Portal[0m[38;5;12m (https://singlecell.broadinstitute.org/single_cell) - Reducing barriers and accelerating single-cell research.[39m
[38;5;12m- [39m[38;5;14m[1mAllen Brain Map - Transcriptomics Explorer[0m[38;5;12m (http://celltypes.brain-map.org/rnaseq/human_m1_10x) - Atlas of human and mouse transcriptomic cell types.[39m
[38;5;12m- [39m[38;5;14m[1mSingle Cell VR[0m[38;5;12m (https://singlecellvr.herokuapp.com/) - Interactive visualization of single-cell data in virtual reality.[39m
[38;5;12m- [39m[38;5;14m[1mSPRING[0m[38;5;12m (https://kleintools.hms.harvard.edu/tools/springViewer_1_6_dev.html?datasets/mouse_HPCs/basal_bone_marrow/full) - A tool for uncovering high-dimensional structure in single-cell gene expression data.[39m
[38;5;12m- [39m[38;5;14m[1mSTART[0m[38;5;12m (https://kcvi.shinyapps.io/START/) -  Shiny Transcriptome Analysis Resource Tool allows users to visualize RNA-seq data starting with count data.[39m
[38;5;12m- [39m[38;5;14m[1miSEE[0m[38;5;12m (https://marionilab.cruk.cam.ac.uk/iSEE_allen/) - The Interactive SummarizedExperiment Explorer.[39m
[38;5;12m- [39m[38;5;14m[1mTISCH[0m[38;5;12m (http://tisch.comp-genomics.org/home/) - Tumor Immune Single-cell Hub (TISCH) is a scRNA-seq database focusing on tumor microenvironment.[39m

[38;2;255;187;0m[4mGene expression matrices[0m
[38;5;12m- [39m[38;5;14m[1mEBI Single Cell Expression Atlas[0m[38;5;12m (https://www.ebi.ac.uk/gxa/sc/home) - Single cell gene expression across species.[39m
[38;5;12m- [39m[38;5;14m[1mMORPHEUS[0m[38;5;12m (https://software.broadinstitute.org/morpheus/) - Versatile matrix visualization and analysis software.[39m
[38;5;12m- [39m[38;5;14m[1mClustergrammer[0m[38;5;12m (https://maayanlab.cloud/clustergrammer/) - Visualize high-dimensional data as interactive hierarchically clustered heatmaps.[39m

[38;2;255;187;0m[4mMicroscopy[0m
[38;5;12m- [39m[38;5;14m[1mIONpath MIBItracker[0m[38;5;12m (https://www.ionpath.com/mibitracker/) - Slide and image data.[39m
[38;5;12m- [39m[38;5;14m[1mAvivator[0m[38;5;12m (http://avivator.gehlenborglab.org/) - A lightweight "batteries-included" WebGL viewer for remote imaging data in Bio-Formats Zarr or OME-TIFF format.[39m

[38;2;255;187;0m[4mConnectomics[0m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mneuroglancer[0m[38;5;12m [39m[38;5;12m(https://hemibrain-dot-neuroglancer-demo.appspot.com/#!gs://neuroglancer-janelia-flyem-hemibrain/v1.0/neuroglancer_demo_states/kc_apl_mpn1.json)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mTool[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mvisualization[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mhighly[39m[38;5;12m [39m[38;5;12mdetailed[39m[38;5;12m [39m[38;5;12mmaps[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mneuronal[39m[38;5;12m [39m[38;5;12mconnectivity[39m[38;5;12m [39m[38;5;12min[39m
[38;5;12mthe[39m[38;5;12m [39m[38;5;12mfly[39m[38;5;12m [39m[38;5;12mbrain.[39m
[38;5;12m- [39m[38;5;14m[1mAllen Mouse Brain Connectivity Atlas[0m[38;5;12m (http://connectivity.brain-map.org/) - A high-resolution map of neural connections in the mouse brain.[39m
[38;5;12m- [39m[38;5;14m[1mFlyWire[0m[38;5;12m (https://flywire.ai/) - A human-AI collaboration to map the fly connectome.[39m


[38;2;255;187;0m[4mMetabolomics[0m
[38;5;12m- [39m[38;5;14m[1mMetaspace[0m[38;5;12m (https://metaspace2020.eu/) - A platform for metabolite annotation of imaging mass spectrometry data.[39m


[38;2;255;187;0m[4mMass Spectrometry[0m
[38;5;12m- [39m[38;5;14m[1mCytosplore[0m[38;5;12m (https://www.cytosplore.org/) - Cytosplore is an interactive visual analysis system for the analysis of mass cytometry data.[39m


[38;2;255;187;0m[4mPopulations[0m
[38;5;12m- [39m[38;5;14m[1mNextstrain[0m[38;5;12m (https://nextstrain.org/) - Real-time tracking of virus evolution.[39m
[38;5;12m- [39m[38;5;14m[1mInstitute for Health Metrics and Evaluation[0m[38;5;12m (http://www.healthdata.org/results/data-visualizations) - Visualizations of disease worldwide.[39m
[38;5;12m- [39m[38;5;14m[1mLifespans[0m[38;5;12m (http://www.cotrino.com/lifespan/) - Visualization of the lifespans of multiple species.[39m
[38;5;12m- [39m[38;5;14m[1mLife Expectancy[0m[38;5;12m (http://projects.flowingdata.com/life-expectancy/) - Life expectancies around the world, 1960 to 2009.[39m


[38;2;255;187;0m[4mMedicine[0m
[38;5;12m- [39m[38;5;14m[1mSnake Oil Supplements[0m[38;5;12m (http://informationisbeautiful.net/visualizations/snake-oil-scientific-evidence-for-nutritional-supplements-vizsweet/) - Scientific evidence for popular health supplements.[39m
[38;5;12m- [39m[38;5;14m[1mSieveSifter[0m[38;5;12m (http://sieve.fredhutch.org/viz/index.html?study=VTN503&protein=gag&reference=MRK_B_Ad5) - Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.[39m
