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