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Run the test data as the flowing:
**step1**
python main_netMHCpan_pipe.py --preponly -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun -c 1 2 -E 8 9 10
INFO: Annovar r…
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Dear All,
I am running vcf-expression annotator via this command
vcf-expression-annotator $VCF simple_gene_counts.txt custom gene --id-column Geneid --expression-column gerald_C1TD1ACXX_8_ACAGTG.sor…
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Hello
I have a set of vcf files (SNVs) from patients who have responded to chemotherapy versus a set of patients who have not responded.
I want to quantify the neoantigen load in the tumors ,can…
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Mockup and rough R code are attached. Key features:
- "binning" of peptides into predefined categories/tiers
- revision that exposes more data in a more interpretable manner
As discussed, step 1…
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Hi
I read the program parameters, but I could not understand parameters c(colregions) .
In the example,python NeoPredPipe.py -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n Test…
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Hello
Our cluster computing group has installed your software via docker on our server like below which directed me to R environment
```
module load singularity/3.2.1
singularity pull antigen.…
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Hi
PeptideMatch is only necessary if one wishes to check predicted epitopes for novelty against a reference proteome.
Meanwhile, you advise the use of PeptideMatch for indel predictions, to filter o…
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Hello,
As shown below, I got some error messages when running Step 3 for neoantigen prediction. I run "predict_binding.py" separately and the example commands in the README file. Everything is workin…
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Analyses generally will be separated into three groups- IDH wt, IDH mut, IDH mut 1p/19q
Include exomes when we can- number in abstract must be high as possible
@roelverhaak made a list of items t…
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#### What analysis module should be updated and why?
PBTA vs TCGA TMB analysis In the works by @cansavvy #548 based on #551 and/or #257
#### What changes need to be made? Please provide enoug…