Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Overview of PANOPLY architecture and the various tasks that constitute the complete workflow.

Data availability

Tutorial data are accessible online at Zenodo (, GitHub ( and Terra ( Data for the CPTAC LUAD and BRCA studies are accessible online at Terra ( More detailed information is provided in Supplementary Table 1.

Code availability

All code is accessible online at Zenodo (, GitHub ( and Terra ( More detailed information is provided in Supplementary Table 1.


  1. 1.

    Mertins, P. et al. Nature 534, 55–62 (2016).

    CAS  Article  Google Scholar 

  2. 2.

    Zhang, B. et al. Nature 513, 382–387 (2014).

    CAS  Article  Google Scholar 

  3. 3.

    Gillette, M. A. et al. Cell 182, 200–225.e35 (2020).

    CAS  Article  Google Scholar 

  4. 4.

    Krug, K. et al. Cell 183, 1–21 (2020).

    Article  Google Scholar 

  5. 5.

    Subramanian, A. et al. Cell 171, 1437–1452.e17 (2017).

    CAS  Article  Google Scholar 

  6. 6.

    Blumenberg, L. et al. Preprint at bioRxiv (2019).

  7. 7.

    Krug, K. et al. Mol. Cell. Proteomics 18, 576–593 (2019).

    CAS  Article  Google Scholar 

  8. 8.

    Subramanian, A. et al. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).

    CAS  Article  Google Scholar 

  9. 9.

    Yoshihara, K. et al. Nat. Commun. 4, 2612 (2013).

    Article  Google Scholar 

  10. 10.

    Aran, D., Hu, Z. & Butte, A. J. Genome Biol. 18, 220 (2017).

    Article  Google Scholar 

Download references


This work was supported by grants from National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium grants NIH/NCI U24CA210979 (to D.R.M. and G.G.) and NIH/NCI U24-CA210986 and NIH/NCI U01 CA214125 (to S.A.C.).

Author information




The project was conceived by D.R.M., S.A.C., G.G. and C.B. Software design, implementation, testing and documentation was executed by D.R.M., M.M., R.K., K.K., K.E.C., D.H. and K.R.C. D.R.M. and K.K. wrote the manuscript, with input and revisions from all authors.

Corresponding author

Correspondence to D. R. Mani.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Methods thanks the anonymous reviewers for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Table 1

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Mani, D.R., Maynard, M., Kothadia, R. et al. PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis. Nat Methods 18, 580–582 (2021).

Download citation


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing