Oncoscape
Accelerate your research
Maximize the potential of your clinical and genomic data by combining it with best-in-class analysis,
reference data sets and domain-specific visualizations. To request training or a custom solution contact us at
contact@oncoscape.org.
Analysis
- Reliable
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All data manipulation and augmentation is done using established open source libraries and public
stores with citations.
- Reproducible
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All analysis in Oncoscape is fully reproducible. Pause, rewind and interrogate every variable and
result.
Data
- Public Data Sets
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Explore The Cancer Genome Atlas (TCGA) and other curated data from our growing list of reference
libraries.
- Private Data Upload
- Securely manage and analyze your clinical and genomics data, then share results with colleges.
- Gene Sets
- Select from thousands of curated gene sets from MSigDB or create your own.
- Pathways
- Select from thousands of the top-level pathways from Reactome, PathwayCommons, and more.
Visualizations
- Clinical Dashboard
- Compare cohorts at a glance.
- Spreadsheet
- Sort and export your data, cohorts and genes of interest in tabular format.
- Matrix Decomposition
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Visualize the inherent spatial structure of high dimensional datasets in 3D. With 13 fully
customizable linear dimension reduction algorithm, select from 5 variants of PCA, Factor Analysis,
LDA, SVD and more.
- Heat map
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Sort, group and visualize your data using 7 agglomerative clustering algorithms in conjunction with 20
distance metrics. Leverage dendrogram to sub select populations of samples or markers for further
investigation.
- Genome
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Identify chromosomal regions of interest by projecting your data onto a visual representation of the
genome. Overlay CNV, Gistic or expression data along with Topically Aligned Domains and Cytobands.
Explore thousands of curated gene sets or create your own.
- Chromosome
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Compare datasets at the chromosomal level with circos and linear visualizations. Overlay pathways or
topically aligned domains.
- Pathways
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Overlay your data on over 5,900 pathways curated from Kegg, Panther, Reactome, SMPDB, WikiPathways and
Pathway Commons.
- Survival
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Estimate and compare survival rates for patient populations using Kaplin Kaplan-Meier, Nelson-Aalen,
Aalen, Weibulland Cox models.
- Hazard
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Estimate and compare hazard rates for patient populations using Kaplin Kaplan-Meier, Nelson-Aalen,
Aalen, Weibull and Cox models.
- Timelines
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Visualize patterns in time series data with an interactive swimmer plot. Sort, group and highlight
patients using clinical attributes.
- Box + Whisker
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Gain insights into the distribution of your data by visualizing the minimum, first quartile, median,
3rd quartile and maximum values.
- Force Directed Graph
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Visualize graph data in three-dimensions using a class of algorithms called "force directed graphs. "
These algorithmsuse the number and strength of connections to position nodes.
- Edges
- Connect multiple graphs with edges. Link tumor/normal samples or visualize mutations.