Genomics

• Gosling - A grammar-based toolkit for scalable and interactive genomics data visualization.

3D Genomics

• HiPiler - A tool for visually exploring and aggregating reoccurring patterns (like loops, TADs, etc.) in Hi-C maps.

Epigenomics

• Peax (⭐63) - Interactive visual pattern exploration in epigenomic data using unsupervised deep representation learning.

Mass Spectrometry / Gene expression matrices

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

Genomics

• Coessentiality - A genome-wide almanac of co-essential modules assigns function to uncharacterized genes.

(Non-spatial) Transcriptomics / Gene expression matrices

• EBI Single Cell Expression Atlas - Single cell gene expression across species.

• MORPHEUS - Versatile matrix visualization and analysis software.

• Clustergrammer - Visualize high-dimensional data as interactive hierarchically clustered heatmaps.

(Non-spatial) Transcriptomics

• TISCH - Tumor Immune Single-cell Hub (TISCH) is a scRNA-seq database focusing on tumor microenvironment.

Cancer

• cBioPortal for Cancer Genomics - Visualization, analysis and download of large-scale cancer genomics data sets.

• Oncoscape - An integrated suite of analysis tools for users to explore hypotheses related to molecular and clinical data.

Genomics

• 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.

3D Genomics

• TADkit - 3D genome browser and TADbit front-end.

Proteomics

• COSMIC-3D - A platform for understanding cancer mutations in the context of 3D protein structure.

Spatial transcriptomics

• 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.

• Giotto Viewer - A web-based visualization package for spatial transcriptomic data.

(Non-spatial) Transcriptomics

• cellxgene - An interactive explorer for single-cell transcriptomics data.

• UCSC Cell Browser - An interactive viewer for single-cell expression.

• ASAP - A collaborative portal to analyze single-cell transcriptomics data.

• 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.

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.

Connectomics / Gene expression matrices

• Allen Mouse Brain Connectivity Atlas - A high-resolution map of neural connections in the mouse brain.

• FlyWire - A human-AI collaboration to map the fly connectome.

Metabolomics / Gene expression matrices

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

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.

Cancer

• Signal - Mutational signatures extracted from cancer samples and isogenic cell-based experiments.

(Non-spatial) Transcriptomics

• SCope - A visualization tool for large-scale scRNA-seq datasets.

Connectomics / Gene expression matrices

• neuroglancer - Tool for visualization of highly detailed maps of neuronal connectivity in the fly brain.

Cancer

• ExploSig - Interactive visualization of mutational signatures and clinical data.

Genomics

• GeneMANIA - Helps predict the function of genes and gene sets.

• Mutaframe - Visualize variants of the human genome.

Epigenomics

• GIVe - Epigenome and genome interaction.

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.

• iCoMut Beta for FireBrowse - Interactive exploration of mutation rates, mutation signatures, clinical data, gene mutations.

• MAGI - Visualization and collaborative annotation of genomic aberrations.

• 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.

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.

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.

• 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

• EzMol - Visualisation and image production of protein and nucleic acid structures.

• LiteMol - Visualization of large-scale macromolecular structure data.

(Non-spatial) Transcriptomics

• L1000FWD - Large-scale visualization of drug-induced transcriptomic signatures.

Populations / Gene expression matrices

• 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.