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kaistomics / DeepNeo

identification of immunogenic neoepitopes
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Extended Data #1

Open MMCXXVI opened 1 year ago

MMCXXVI commented 1 year ago

Good day!

In your paper, you compared the impact of DeepNeo-MHC, NetMHCpan, and MixMHCpred on MHC binding prediction using different extended data collected from multiple publications, as shown in Figure 1 c and d.

However, I noticed that I couldn't find any annotations or download links for these extended data in the Supplementary information of your paper, the webserver page, or this repository, because it is too trivial to share, or did I miss it somewhere?

Thank you a lot.

Cheers, guangfu xue

malachig commented 1 year ago

In the DeepNEO paper:

Code availability
Codes for implementing prediction of peptide-MHC binding and prediction of immunogenicity are deposited at https://github.com/kaistomics/DeepNeo.

https://www.nature.com/articles/s41588-022-01273-y

The authors have publicly attested that they will share this code. And it did indeed exist at this location previously, but has apparently now been removed.

MMCXXVI commented 1 year ago

In the DeepNEO paper:

Code availability
Codes for implementing prediction of peptide-MHC binding and prediction of immunogenicity are deposited at https://github.com/kaistomics/DeepNeo.

https://www.nature.com/articles/s41588-022-01273-y

The authors have publicly attested that they will share this code. And it did indeed exist at this location previously, but has apparently now been removed.

Indeed, two months ago, this GitHub repository contained the relevant model code but lacked the dataset files. However, at present, the repository has been completely emptied, with even the associated code being deleted. If other researchers are unable to reproduce this work, coupled with the fact that the repository was cleared by the author, there are legitimate reasons to question the validity of this research.