jaeswift-website/api/data/awesomelist/keller-mark--awesome-biological-visualizations.json

{"slug": "keller-mark--awesome-biological-visualizations", "title": "Biological Visualizations", "description": "A list of web-based interactive biological data visualizations.", "github_url": "https://github.com/keller-mark/awesome-biological-visualizations", "stars": "99", "tag": "Miscellaneous", "entry_count": 84, "subcategory_count": 2, "subcategories": [{"name": "General", "parent": "", "entries": [{"name": "Cancer", "url": "#cancer", "description": ""}, {"name": "Genomics", "url": "#genomics", "description": ""}, {"name": "3D Genomics", "url": "#3d-genomics", "description": ""}, {"name": "Metagenomics", "url": "#metagenomics", "description": ""}, {"name": "Epigenomics", "url": "#epigenomics", "description": ""}, {"name": "Proteomics", "url": "#proteomics", "description": ""}, {"name": "Spatial transcriptomics", "url": "#spatial-transcriptomics", "description": ""}, {"name": "(Non-spatial) Transcriptomics", "url": "#non-spatial-transcriptomics", "description": ""}, {"name": "Microscopy", "url": "#microscopy", "description": ""}, {"name": "Connectomics", "url": "#connectomics", "description": ""}, {"name": "Metabolomics", "url": "#metabolomics", "description": ""}, {"name": "Mass Spectrometry", "url": "#mass-spectrometry", "description": ""}, {"name": "Populations", "url": "#populations", "description": ""}, {"name": "Medicine", "url": "#medicine", "description": ""}, {"name": "COSMIC Cancer Browser", "url": "https://cancer.sanger.ac.uk/cosmic/browse/tissue", "description": "Browse COSMIC data by tissue type and histology."}, {"name": "UCSC Xena", "url": "https://xenabrowser.net/", "description": "Explore functional genomic data sets for correlations between genomic and/or phenotypic variables."}, {"name": "cBioPortal for Cancer Genomics", "url": "http://www.cbioportal.org/", "description": "Visualization, analysis and download of large-scale cancer genomics data sets."}, {"name": "iCoMut Beta for FireBrowse", "url": "http://firebrowse.org/iCoMut/", "description": "Interactive exploration of mutation rates, mutation signatures, clinical data, gene mutations."}, {"name": "MAGI", "url": "http://magi.brown.edu", "description": "Visualization and collaborative annotation of genomic aberrations."}, {"name": "ExploSig", "url": "http://explosig.lrgr.io", "description": "Interactive visualization of mutational signatures and clinical data."}, {"name": "Race, Gender, and Age in TCGA", "url": "https://www.enpicom.com/visual-lab/tcga-visual-exploration-gender-race-age/", "description": "An interactive visualization of patient gender, race, and age in The Cancer Genome Atlas (TCGA) dataset."}, {"name": "OASISPRO", "url": "http://tinyurl.com/oasispro", "description": "Omics analysis tool for clinical phenotype prediction."}, {"name": "Signal", "url": "https://signal.mutationalsignatures.com/", "description": "Mutational signatures extracted from cancer samples and isogenic cell-based experiments."}, {"name": "Oncoscape", "url": "https://oncoscape.sttrcancer.org/", "description": "An integrated suite of analysis tools for users to explore hypotheses related to molecular and clinical data."}, {"name": "UCSC Genome Browser", "url": "https://genome.ucsc.edu/", "description": "Interactively visualize genomic data."}, {"name": "Ensembl", "url": "http://www.ensembl.org", "description": "A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation."}, {"name": "IMP: Integrative Multi-species Prediction", "url": "http://imp.princeton.edu/", "description": "Analyze your experimental results in the functional context of gene-gene networks from multiple organisms."}, {"name": "PLACNETw", "url": "https://castillo.dicom.unican.es/ex1/?unique=58f731fec480a", "description": "A graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets."}, {"name": "PhyD3", "url": "https://phyd3.bits.vib.be/view.php?id=91162629d258a876ee994e9233b2ad87\\&f=xml", "description": "A phylogenetic tree viewer."}, {"name": "Archaeopteryx", "url": "http://www.phyloxml.org/archaeopteryx-js/bcl2_js.html", "description": "Visualization, analysis, and editing of phylogenetic trees."}, {"name": "GeneMANIA", "url": "http://genemania.org/", "description": "Helps predict the function of genes and gene sets."}, {"name": "Mutaframe", "url": "http://deogen2.mutaframe.com/", "description": "Visualize variants of the human genome."}, {"name": "Coessentiality", "url": "http://coessentiality.net", "description": "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes."}, {"name": "Gosling", "url": "https://gosling.js.org", "description": "A grammar-based toolkit for scalable and interactive genomics data visualization."}, {"name": "HiGlass", "url": "http://higlass.io/", "description": "A tool for exploring genomic contact matrices and tracks."}, {"name": "HiPiler", "url": "http://hipiler.higlass.io/", "description": "A tool for visually exploring and aggregating reoccurring patterns (like loops, TADs, etc.) in Hi-C maps."}, {"name": "Delta", "url": "http://delta.big.ac.cn/", "description": "An integrative analysis and visualization platform for 3D genome."}, {"name": "Juicebox", "url": "http://aidenlab.org/juicebox/", "description": "Visualization for Hi-C data."}, {"name": "TADkit", "url": "http://sgt.cnag.cat/3dg/tadkit/demo.h/index.html#!/project/dataset?conf=assets%2Fexamples%2Fconf.json", "description": "3D genome browser and TADbit front-end."}, {"name": "Metaviz", "url": "http://metaviz.cbcb.umd.edu/", "description": "Interactive statistical and visual analysis of metagenomic data."}, {"name": "Malaria Cell Atlas", "url": "https://www.sanger.ac.uk/science/tools/mca/mca/", "description": "Explore how genes are expressed across more than 500 individual Plasmodium parasites."}, {"name": "Epiviz", "url": "http://epiviz.cbcb.umd.edu/4/", "description": "Interactive visual analytics for functional genomics data."}, {"name": "GIVe", "url": "https://mcf7.givengine.org/", "description": "Epigenome and genome interaction."}, {"name": "WashU Epigenome Browser", "url": "http://epigenomegateway.wustl.edu/", "description": "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."}, {"name": "Clustergrammer CCLE Explorer", "url": "https://maayanlab.github.io/CCLE_Clustergrammer/", "description": "Browse relative mRNA expression data for cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) by tissue of origin using Clustergrammer."}, {"name": "Peax", "url": "https://github.com/Novartis/peax", "description": "Interactive visual pattern exploration in epigenomic data using unsupervised deep representation learning.", "stars": "63"}, {"name": "COSMIC-3D", "url": "https://cancer.sanger.ac.uk/cosmic3d/protein/EGFR", "description": "A platform for understanding cancer mutations in the context of 3D protein structure."}, {"name": "EzMol", "url": "http://www.sbg.bio.ic.ac.uk/\\~ezmol/", "description": "Visualisation and image production of protein and nucleic acid structures."}, {"name": "LiteMol", "url": "https://webchemdev.ncbr.muni.cz/LiteMol/", "description": "Visualization of large-scale"}, {"name": "Vitessce", "url": "http://vitessce.io", "description": "Visual integration tool for exploration of spatial single-cell experiment data."}, {"name": "Brain mRNA Isoform Atlas", "url": "https://isoformatlas.com/", "description": "Visualize cell type signatures of alternative splicing in postnatal development."}, {"name": "AlzMap", "url": "https://alzmap.org/", "description": "Spatial transcriptomics in Alzheimer's disease."}, {"name": "Loom Viewer", "url": "http://loom.linnarssonlab.org/dataset/cells/osmFISH/osmFISH_SScortex_mouse_all_cells.loom/NrBEoXQGhYDYoAYLRARigZlRgTDpAtAgFhRnSyg0Wrt1rUVuAHYlCYAOD5AzOo3qNmMAJy8ctaeWAYS0jvNoNqotpO6TSioZgmqmLCTJhNt0ebPCpgAWkQA6RJjgkxYxLkwlMrAKxIjr5wbv7\\~iKxcaLj\\~0AIkULhK\\~DAscpwZxGZJ_LIgigB2AK4ANqVKHIbquqi10LVKsgIl5RxyybFQPIGYGAi4yey4PGjDArjsaAgYaBOJaDy4A3i0C4G4EgbUEmiJmIwYmMnm2E0QQA", "description": "Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format."}, {"name": "TissUUmaps", "url": "https://tissuumaps.research.it.uu.se/", "description": "Interactive visualization of large-scale spatial gene expression and tissue morphology data."}, {"name": "Giotto Viewer", "url": "http://spatialgiotto.rc.fas.harvard.edu/giotto.viewer.html", "description": "A web-based visualization package for spatial transcriptomic data."}, {"name": "cellxgene", "url": "https://www.kidneycellatlas.org/mature-kidney-immune", "description": "An interactive explorer for single-cell transcriptomics data."}, {"name": "UCSC Cell Browser", "url": "http://cells.ucsc.edu/?ds=cortex-dev", "description": "An interactive viewer for single-cell expression."}, {"name": "L1000FWD", "url": "http://amp.pharm.mssm.edu/L1000FWD/", "description": "Large-scale visualization of drug-induced transcriptomic signatures."}, {"name": "ASAP", "url": "https://asap.epfl.ch/", "description": "A collaborative portal to analyze single-cell transcriptomics data."}, {"name": "SCope", "url": "http://scope.aertslab.org/", "description": "A visualization tool for large-scale scRNA-seq datasets."}, {"name": "Mouse Brain Atlas", "url": "http://mousebrain.org/", "description": "Atlas of cell types from the Linnarsson Lab."}, {"name": "Broad Institute Single Cell Portal", "url": "https://singlecell.broadinstitute.org/single_cell", "description": "Reducing barriers and accelerating single-cell research."}, {"name": "Allen Brain Map - Transcriptomics Explorer", "url": "http://celltypes.brain-map.org/rnaseq/human_m1_10x", "description": "Atlas of human and mouse transcriptomic cell types."}, {"name": "Single Cell VR", "url": "https://singlecellvr.herokuapp.com/", "description": "Interactive visualization of single-cell data in virtual reality."}, {"name": "SPRING", "url": "https://kleintools.hms.harvard.edu/tools/springViewer_1_6_dev.html?datasets/mouse_HPCs/basal_bone_marrow/full", "description": "A tool for uncovering high-dimensional structure in single-cell gene expression data."}, {"name": "START", "url": "https://kcvi.shinyapps.io/START/", "description": "Shiny Transcriptome Analysis Resource Tool allows users to visualize RNA-seq data starting with count data."}, {"name": "iSEE", "url": "https://marionilab.cruk.cam.ac.uk/iSEE_allen/", "description": "The Interactive SummarizedExperiment Explorer."}, {"name": "TISCH", "url": "http://tisch.comp-genomics.org/home/", "description": "Tumor Immune Single-cell Hub (TISCH) is a scRNA-seq database focusing on tumor microenvironment."}]}, {"name": "Gene expression matrices", "parent": "(Non-spatial) Transcriptomics", "entries": [{"name": "EBI Single Cell Expression Atlas", "url": "https://www.ebi.ac.uk/gxa/sc/home", "description": "Single cell gene expression across species."}, {"name": "MORPHEUS", "url": "https://software.broadinstitute.org/morpheus/", "description": "Versatile matrix visualization and analysis software."}, {"name": "Clustergrammer", "url": "https://maayanlab.cloud/clustergrammer/", "description": "Visualize high-dimensional data as interactive hierarchically clustered heatmaps."}, {"name": "IONpath MIBItracker", "url": "https://www.ionpath.com/mibitracker/", "description": "Slide and image data."}, {"name": "Avivator", "url": "http://avivator.gehlenborglab.org/", "description": "A lightweight \"batteries-included\" WebGL viewer for remote imaging data in Bio-Formats Zarr or OME-TIFF format."}, {"name": "neuroglancer", "url": "https://hemibrain-dot-neuroglancer-demo.appspot.com/#!gs://neuroglancer-janelia-flyem-hemibrain/v1.0/neuroglancer_demo_states/kc_apl_mpn1.json", "description": "Tool for visualization of highly detailed maps of neuronal connectivity in the fly brain."}, {"name": "Allen Mouse Brain Connectivity Atlas", "url": "http://connectivity.brain-map.org/", "description": "A high-resolution map of neural connections in the mouse brain."}, {"name": "FlyWire", "url": "https://flywire.ai/", "description": "A human-AI collaboration to map the fly connectome."}, {"name": "Metaspace", "url": "https://metaspace2020.eu/", "description": "A platform for metabolite annotation of imaging mass spectrometry data."}, {"name": "Cytosplore", "url": "https://www.cytosplore.org/", "description": "Cytosplore is an interactive visual analysis system for the analysis of mass cytometry data."}, {"name": "Nextstrain", "url": "https://nextstrain.org/", "description": "Real-time tracking of virus evolution."}, {"name": "Institute for Health Metrics and Evaluation", "url": "http://www.healthdata.org/results/data-visualizations", "description": "Visualizations of disease worldwide."}, {"name": "Lifespans", "url": "http://www.cotrino.com/lifespan/", "description": "Visualization of the lifespans of multiple species."}, {"name": "Life Expectancy", "url": "http://projects.flowingdata.com/life-expectancy/", "description": "Life expectancies around the world, 1960 to 2009."}, {"name": "Snake Oil Supplements", "url": "http://informationisbeautiful.net/visualizations/snake-oil-scientific-evidence-for-nutritional-supplements-vizsweet/", "description": "Scientific evidence for popular health supplements."}, {"name": "SieveSifter", "url": "http://sieve.fredhutch.org/viz/index.html?study=VTN503\\&protein=gag\\&reference=MRK_B_Ad5", "description": "Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials."}]}], "name": ""}