Cancer
- 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.
- 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.
- ASAP - A collaborative portal to analyze single-cell transcriptomics data.
- 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
- Avivator - A lightweight "batteries-included" WebGL viewer for remote imaging data in Bio-Formats Zarr or OME-TIFF format.
Connectomics / Gene expression matrices
- 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
- SieveSifter - Tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.
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