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awesome-biological-visualizations

A list of web-based interactive biological data visualizations.
https://github.com/keller-mark/awesome-biological-visualizations

Last synced: 3 days ago
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  • Spatial transcriptomics

    • Giotto Viewer - A web-based visualization package for spatial transcriptomic data.
    • 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.
    • Vitessce - Visual integration tool for exploration of spatial single-cell experiment data.
    • TissUUmaps - Interactive visualization of large-scale spatial gene expression and tissue morphology data.
    • Vitessce - Visual integration tool for exploration of spatial single-cell experiment data.

  • 3D Genomics

    • 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.
    • HiGlass - A tool for exploring genomic contact matrices and tracks.
    • Delta - An integrative analysis and visualization platform for 3D genome.
    • Juicebox - Visualization for Hi-C data.
    • Delta - An integrative analysis and visualization platform for 3D genome.

  • 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.
    • 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

  • 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.

  • (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.
      • L1000FWD - Large-scale visualization of drug-induced transcriptomic signatures.
      • SCope - A visualization tool for large-scale scRNA-seq datasets.
      • L1000FWD - Large-scale visualization of drug-induced transcriptomic signatures.
      • SPRING - A tool for uncovering high-dimensional structure in single-cell gene expression data.

    • Gene expression matrices

  • 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.
    • PhyD3 - A phylogenetic tree viewer.
    • 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.
    • 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.
    • Ensembl - A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
    • Coessentiality - A genome-wide almanac of co-essential modules assigns function to uncharacterized genes.

  • Microscopy

    • Gene expression matrices

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

  • Connectomics

    • Gene expression matrices

  • Metabolomics

    • Gene expression matrices

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

  • Mass Spectrometry

    • Gene expression matrices

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

  • Populations

  • Medicine

    • Gene expression matrices

      • Snake Oil Supplements - Scientific evidence for popular health supplements.
      • SieveSifter - Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.
      • SieveSifter - Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.
      • SieveSifter - Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.
Programming Languages
Jupyter Notebook 2
Categories
(Non-spatial) Transcriptomics 20 Genomics 18 Cancer 10 Spatial transcriptomics 9 3D Genomics 8 Epigenomics 5 Populations 5 Medicine 4 Proteomics 3 Connectomics 3 Microscopy 3 Metagenomics 3 Mass Spectrometry 1 Metabolomics 1
Sub Categories
Gene expression matrices 20
Keywords
sequential-data 1 pattern-search 1 interactive-machine-learning 1 epigenomics 1 deep-learning 1 data-visualization 1 autoencoder 1