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.