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-sttr@fredhutch.org.

Analysis

Reliable

All data manipulation and augmentation is done using established open source libraries and public stores with citations.

Reproducible

All analysis in Oncoscape is fully reproducible. Pause, rewind and interrogate every variable and result.

Data

Public Data Sets

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 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

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

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

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

Compare datasets at the chromosomal level with circos and linear visualizations. Overlay pathways or topically aligned domains.

Pathways

Overlay your data on over 5,900 pathways curated from Kegg, Panther, Reactome, SMPDB, WikiPathways and Pathway Commons.

Survival

Estimate and compare survival rates for patient populations using Kaplin Kaplan-Meier, Nelson-Aalen, Aalen, Weibulland Cox models.

Hazard

Estimate and compare hazard rates for patient populations using Kaplin Kaplan-Meier, Nelson-Aalen, Aalen, Weibull and Cox models.

Timelines

Visualize patterns in time series data with an interactive swimmer plot. Sort, group and highlight patients using clinical attributes.

Box + Whisker

Gain insights into the distribution of your data by visualizing the minimum, first quartile, median, 3rd quartile and maximum values.

Force Directed Grap

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.