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

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

Data availability

Tutorial data are accessible online at Zenodo (https://doi.org/10.5281/zenodo.4728140), GitHub (https://github.com/broadinstitute/PANOPLY) and Terra (https://app.terra.bio/). Data for the CPTAC LUAD and BRCA studies are accessible online at Terra (https://app.terra.bio/). More detailed information is provided in Supplementary Table 1.

Code availability

All code is accessible online at Zenodo (https://doi.org/10.5281/zenodo.4728140), GitHub (https://github.com/broadinstitute/PANOPLY) and Terra (https://app.terra.bio/). More detailed information is provided in Supplementary Table 1.

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Acknowledgements

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.).

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Authors and Affiliations

  1. Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    D. R. Mani, Myranda Maynard, Ramani Kothadia, Karsten Krug, Karen E. Christianson, Karl R. Clauser & Steven A. Carr

  2. Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    David Heiman, Chet Birger & Gad Getz

  3. Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, MA, USA

    Gad Getz

  4. Harvard Medical School, Boston, MA, USA

    Gad Getz

Authors
  1. D. R. Mani
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  2. Myranda Maynard
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  3. Ramani Kothadia
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  4. Karsten Krug
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  5. Karen E. Christianson
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  6. David Heiman
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  7. Karl R. Clauser
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  8. Chet Birger
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  9. Gad Getz
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  10. Steven A. Carr
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Contributions

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.

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Competing interests

The authors declare no competing interests.

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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

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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). https://doi.org/10.1038/s41592-021-01176-6

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