-
Hi,
I use the following code to predict neoantigen :
```
NeoPredPipe.py -I ./test/ -H ./TCGA_HLA_typing.txt -o ./test_results -n TCGA-02-0047-01A -c 0 -E 8 9 10 -x exp/
```
The `test_result` di…
-
Failed 4 times, for the same reason.
In the current WES repo, I got this for two different tumors, but the same normal:
```
2c/ecc9df RunNeoantigen s_C_WNLXAP_P001_d__s_C_WNLXAP_N001_d FAILED 1 1…
-
So that we can run @iskandr's pipeline on it and get a short-list of "neoepitopes" that we can work our way through.
Submitted MC38B cell pellets (as well as PBMCs from B6 mouse as our normal) to G…
-
For example, from this paper: [Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing](https://www.ncbi.nlm.nih.gov/pubmed/25428506):
Gene | Peptide | MHC allel…
-
Hello,
I'm facing this issue wtith recent pVACtool 2.0.0, I can see genotype info in VCF file (attached here).
Could you please have a look and let me know If i'm missing anything here.
Run c…
-
Hi:
I developed a perl script [NeoPredPipe.install.pl](https://github.com/wangshun1121/NeoPredPipe/blob/master/NeoPredPipe.install.pl) to deploy latest NeoPredPipe, using following command:
```…
-
Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/tangshao2016/neoantigenR
Confirm the following by…
-
Dear professor,
thanks in advance, mnp and complex variant is important, if can not be added depth, it maybe not well evaluated in neoantigen prediction,
thanks a lot
![image](https://user-images.g…
-
Hello NeoPredPipe developers:
I am using the latest version of NeoPredPipe. I cloned the repo two days ago and saw that there are some updates about dectecting type-II HLA neoantigens. But I can't …
-
Dear developers,
Thank you very much for the useful tool. I built Python2.7 with conda, and configure the 'usr_path.ini' file for my environment.
Then I run `python NeoPredPipe.py -I ./Example/i…