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Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape

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Fig. 1: Oncoscape suite of interoperable tools for analysis and visualization.

Data availability

All data were obtained through the GDC8 and UCSC Xena public data portals. Instructions on how to access our REST API for processed data are available on the Oncoscape data documentation site at http://resources.sttrcancer.org/api/.

References

  1. 1.

    Zhu, J. et al. Nat. Methods 6, 239–240 (2009).

    CAS  Article  Google Scholar 

  2. 2.

    Cerami, E. et al. Cancer Discov. 2, 401–404 (2012).

    Article  Google Scholar 

  3. 3.

    Lawrence, M. S. et al. Nature 505, 495–501 (2014).

    CAS  Article  Google Scholar 

  4. 4.

    Cancer Genome Atlas Network. Nature 487, 330–337 (2012).

    Article  Google Scholar 

  5. 5.

    Zhou, X. et al. Nat. Genet. 48, 4–6 (2016).

    CAS  Article  Google Scholar 

  6. 6.

    Kaplan, E. L. & Meier, P. J. Amer. Statist. Assn. 53, 457–481 (1958).

    Article  Google Scholar 

  7. 7.

    Pearson, K. Philos. Mag. 2, 559–572 (1901).

    Article  Google Scholar 

  8. 8.

    Grossman, R. L. et al. N. Engl. J. Med. 375, 1109–1112 (2016).

    Article  Google Scholar 

  9. 9.

    Bolouri, H., Zhao, L. P. & Holland, E. C. Proc. Natl Acad. Sci. USA 113, 5394–5399 (2016).

    CAS  Article  Google Scholar 

  10. 10.

    Cimino, P. J. et al. Acta Neuropathol. Commun. 5, 39 (2017).

    Article  Google Scholar 

Download references

Acknowledgements

We thank P. J. Camino, S. Patwell, and F. Szulzesky for helpful suggestions. We thank P. Porter, P. Nelson, M. Houghton, and E. Mendez for critical review and contribution to use cases during development. Funding was provided by NIH grant U54 CA193461 (E.C.H.). Public visualizations shown in Oncoscape are in whole or part based on data generated by the TCGA Research Network (see URLs).

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L.G.M., H.B., P.S., and E.C.H. conceived the project. M.Z. implemented the final architecture and front-end design of Oncoscape; R.M. contributed to development operations; and L.G.M. handled data management. G.K. and J.Z. generated documentation and testing. E.C.H. and D.H.-G. supervised the project, and E.S. and K.C. provided data.

Corresponding author

Correspondence to Eric C. Holland.

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The authors declare no competing interests.

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Supplementary Note 1, Supplementary Tables 1 and 2, and Supplementary Figures 1–6

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McFerrin, L.G., Zager, M., Zhang, J. et al. Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape. Nat Genet 50, 1203–1204 (2018). https://doi.org/10.1038/s41588-018-0208-7

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