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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…
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Hello NeoPredPipe developers:
I am using the latest version of NeoPredPipe. I cloned the repo two days ago.
I am using Python 2.7.15 and I am on a Linux box
(Linux version 3.10.0-862.14.4.el…
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Hello,
I understand that MANTIS was designed to analyze DNA-based sequencing data, but I'm wondering if RNAseq bam files could be used as input data. Or is there any recommended software for estima…
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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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**Describe the bug**
neoantigen cases 1581, 1582, 1583 have wrong P length in .ali file.
Instead of 10, the peptide length is 9.
**Environment:**
alembick
**To Reproduce**
Steps/commands to …
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**Some of the neaopeptide modelling were not finished successfully**
The _modeller.log_ complaining the alignment and PDB are not matched.
**On alembick:**
- Inputs:
case: _1083_ neopeptide
…
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* pvactools version: **docker://griffithlab/pvactools:1.5.9**
* Python version:
* Operating System:
**Describe the bug**
This is similar or identical to #571, where we hit [this exception](htt…
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I would like to use the ScanNeo pipeline and would like to reproduce the results described in the [paper](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz193/5384…
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Hello,
I'm running into an error with OptiType. I'm pasting the lines from the R.optitype.log file below:
0:00:01.97 Generating binary hit matrix.
Traceback (most recent call last):
File "/u…
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"""
**2. Single somatic MAF file**
• Includes all somatic mutations (point/indels) along with annotation, filtering, FACETS CCFs, neoantigen predictions (neo_* columns from somatic_variants/neoantig…