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I tested on the test dataset of nextneopi (https://github.com/icbi-lab/nextNEOpi). I has a similar session for using the arriba to get the fusion genes. From those fusion genes, it can get the peptide…
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Thank you for sharing this nice toolkit of neoantigen identification!
I have finished the T antigen workflow analyses while some errors occurred in the Interactive Neoantigen Viewer. The table of …
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Hi,
I have been testing pVAC-seq with a few samples. For each sample, I have typically 150-400 somatic PASS mutations, of which ~40-75 are missense variants. I am using quite a new version of pVACt…
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Hello, I am a CWL rookie. I want to use the Immuno.cwl to detect neoantigens. It makes me confused that (https://github.com/genome/analysis-workflows) contains too many CWL processes. Is there a descr…
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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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> But for immunopeptidome, we known those peptides have affinity to HLA, so moPepGen would be a perfect fit for generating custom DB to search for it.
I've been wondering about what you said here. …
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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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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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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…