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SNAF is amazing with its integration of a entire workflow of identification of neoantigen. However, I wonder if there is a way to create custom control dataset? It will be super helpful for researcher…
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When we load modules into a pipeline we fail the linting `pr-commit` checks even though it passed all the linting checks on the module level.
See this for an example: https://github.com/mskcc/NeoAn…
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Reference papers that consider the potential that some peptides actual inhibit immune response:
https://www.jimmunol.org/content/204/1_Supplement/91.15
https://pubmed.ncbi.nlm.nih.gov/33504579/
htt…
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first
/lustre/work/shufan/RD/Software/bcftools/bcftools-1.9/bcftools filter -o /mnt/rorke/work/shufan/Test/NeoAntigen/DNA/19705CS/Nomatch/mid/591097_tumor.filter.vcf -m x -e **'INFO/EAS_AF>0.001 || …
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We need a list of BCOs that can fulfill two main functions:
- [ ] Exemplar BCOs referenced in publications
- [ ] BCOs that have important features for testing to be included in the example DB
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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,
I tested all four modules with the example data, however, only module 1 and 3 finished successfully.
I got the same error as issue #4 in module 2.
As for module 4, despite the log sugg…
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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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Hi, It's a useful tool to rank those predicted neoantigen. But I encountered a bug that I am unable to resolve.
See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/us…