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Hi,
I would like to customize the HLA input, which can be added with the optional argument -C.
I wonder about the pattern of the HLA.txt file that I should prepare for running multiple samples.
Ma…
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Hello, I am having an issue using deephlapan.
I used the docker installation on MacOS. When I run the program on a test peptide or a file of several peptides, it stop at the same step.
First, I get…
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>>> import os,sys
>>> import pandas as pd
>>> import numpy as np
>>> import anndata as ad
>>> import snaf
>>> df = pd.read_csv('/home/ry-03/data/SNAF/altanalyze_output/ExpressionInput/counts.orig…
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I use 10 samples and analysed both by GRCH37 and GRCH38. I conpared the ***filtered.tsv and unfiltered.tsv between GRCH37 and GRCH38. The fusion genes and locations were all different. No same result…
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The suite of tools will need a container to run on nextflow.
Lets call the container `NeoantigenEditing` version `1.0.0`
and push it to: https://hub.docker.com/u/mskcc
Have a look at this file for r…
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Hello,
Is there any plans to implement this workflow https://github.com/griffithlab/anchor_huiming_etal_2023 in pvacseq, described in the https://www.science.org/doi/full/10.1126/sciimmunol.abg2200…
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Hello!
I am testing the pipeline with netMHCpan version 4.1 and all is working as expected.
To convert the neoantigens output to the format required by `NeoRecoPo.py ` should be sufficient to …
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HI:
I want to use NeoRecoPo.py to get Neoantigen Recognition Potential. I used the data you provided to run the project.
**step1:**
`/usr/bin/python NeoPredPipe.py -I ./Example/input_vcfs -H ./Exa…
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https://www.ncbi.nlm.nih.gov/pubmed/26940869
- [ ] [create a issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this checklis…
jjgao updated
6 months ago
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Hi,
I had recently been able to run the nextNEOpi pipeline through (after some minor modification). When looking at the results section I noticed that the `./results/neoantigens/[sample]/Class_II`…
dmgie updated
3 months ago