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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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can only rank the neoantigen by column **'Median Fold Change'**, #726

Closed asmlgkj closed 1 year ago

asmlgkj commented 3 years ago

can I select the neoantigen by the order of pvacseq output. for example , Median MT Score； Median WT Score ；Median Fold Change should I select by the Median Fold Change? and the percentile rank is all NA HH0321050101.filtered.zip

asmlgkj commented 3 years ago

after reading the paper of MHCnuggets. it says many times of immunogenicity in it, does pvacseq ignore the results of that. the paper name is 'High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets'

here is some sentense in it 1 We demonstrated the utility of MHCnuggets as a basic pipeline to analyze mutation immunogenicity, shared predicted IMMs, and the relationship between mutation immunogenicity, driver potential, and immune infiltrates from large-scale cancer patient sequencing data from TCGA
2 We demonstrated the utility of MHCnuggets as a basic pipeline to analyze mutation immunogenicity, shared predicted IMMs, and the relationship between mutation immunogenicity, driver potential, and immune infiltrates from large-scale cancer patient sequencing data from TCGA

asmlgkj commented 3 years ago

thanks a lot

would you consider add tool https://github.com/BGI2016/EPIP to gain the mutation immunogenicity