pauloluniyi / awesome-biological-visualizations

A list of web-based interactive biological visualizations.

Awesome Biological Visualizations

A list of web-based interactive biological visualizations.

If you want to contribute to this list (please do), send a pull request.

Table of Contents

• Cancer
• Genomics
• 3D Genomics
• Metagenomics
• Epigenomics
• Proteomics
• Transcriptomics
• 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.
• iMuSE - Interactive visualization of mutational signatures and hypermutation.
• 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.

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 (Example) - A graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets.
• PhyD3 (Example) - A phylogenetic tree viewer.
• Archaeopteryx (Example) - Visualization, analysis, and editing of phylogenetic trees.
• GeneMANIA - Helps predict the function of genes and gene sets.
• Mutaframe - Visualize variants of the human genome.

3D Genomics

• 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.
• TADkit (Example) - 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.

Proteomics

• COSMIC-3D (Example) - 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 macromolecular structure data.

Transcriptomics

• START - Visualize RNA-seq data.
• ASAP (Example) - Analysis and interactive visualization of single-cell RNA-seq data.
• L1000FWD - Large-scale visualization of drug-induced transcriptomic signatures.

Populations

• Nextstrain - Real-time tracking of virus evolution.
• Institute for Health Metrics and Evaluation - Visualizations of disease worldwide.
• Lifespans - Visualization of the lifespans of multiple species.
• Life Expectancy - Life expectancies around the world, 1960 to 2009.

Medicine

• Snake Oil Supplements? - Scientific evidence for popular health supplements.
• SieveSifter (Example) - Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.

License