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Hi Frank,
First of all congrats and thanks to share this great tool!
I've managed to run it on a small subset of our own patients. We usually test the immunogenicity of neoantigens as longer ep…
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Hello, I'm fairly new to python and I've been trying to use the cohorts library to mainly calculate neoantigens in my tumor samples.
I have each tumor's processed BAM and VCF files but I'm having a d…
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Hi,
I am trying to run pMTnet and notice that each CDR3 always has the same Rank, regardless of which HLA or Peptide it is compared to? These are Neoantigen Peptides so will never have been seen b…
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Hello, thanks for the fantastic tool!
I have been using it for many years, but I am facing a bug I have never encountered.
I am running Neopredpipe for a set of samples, separating them by SNPs an…
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I was very curious to test the performance of mhcnuggets 2.3 on the latest dataset with TESLA validated neoantigen candidates published in Cell ([Key Parameters of Tumor Epitope Immunogenicity
Reveal…
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Hello,
Thank you for such a useful package! I have two queries:
1. When estimating per-gene dNdSCV ratios and confidence intervals using the geneci function, is it possible to calculate a "combine…
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Hello, Fotakis.
I am using neofuse and I encountered an IndexError during the execution of the script `final_out.py`. The error occurs when the script attempts to access elements in a list that app…
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This would be one way to integrate consideration of TCR repertoire data. If a user has TCR data from TILs say, they could use TCRMatch to further prioritize candidates where TCRMatch reports a hit in…
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Hi, I read the your three research papers, These works will surely promote our understanding of tumor evolution.
- The evolution of lung cancer and impact of subclonal selection in TRACERx
- Clonal…