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Hello
thanks for devolving the neofox alogirhtem. I am trying to build a singularity container and then test the data sets. However, i can't figure out why the test data failed. Can you help to ch…
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Ideally we should keep forks of pVACtools and conpair in the umccr GitHub org.
- We currently use this fork of pVACtools inside the [neoantigens conda env](https://github.com/umccr/umccrise/blob/be…
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Thank you for sharing your fasinating work. When I use it, I find all my TCR-pMHC get a very high rank which in your paper represent high possibility for binding. But, in our perspective it can be pos…
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AC:
- Add table to database called neoantigens with columns
- patient_id (foreign_key)
- feature_id (foreign_key)
- gene_id (foreign_key)
- tpm
- Add query to api that
- re…
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Hi, I wanted to express my appreciation for your exceptional work in developing the impressive tool NeoPredPipe. I have a question regarding its functionality: What is the source of the expression col…
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Hi,
We (@ali-harasty and myself) are getting confused by some of the results in the final neoantigen results table e.g.`MHC_Class_I_all_epitopes_ccf_ref` file.
Some of the mutations makes sense …
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> Traceback (most recent call last):
> File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/NeoRecoPo.py", line 135, in
> main()
> File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/NeoRe…
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Dear author,
Thank you for the nice pipeline. I recently ran nextNEOpi pipeline on one sample( DNA tumor, DNA normal and RNA tumor).
The pipeline produced all expected five folders. However, in a…
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Hello I am trying to run the example with this user_ini.path
```
[annovar]
convert2annovar = /home/davide.rambaldi/src/annovar/convert2annovar.pl
annotatevariation = /home/davide.rambaldi/src/an…
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Dear Developers
Your tool is very great. Today I have a new question. I'm using the wrapper tool to model multiple peptides at the same time. The peptides are reported in datafile.tsv and for each …