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There are many neoantigen tools and pipelines out there.
Let's investigate these tools and consider adding them so ours can be the best!
Add all tools/pipelines of interest to the document here:…
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Hi, I read the your three research papers, These works will surely promote our understanding of tumor evolution.
- The evolution of lung cancer and impact of subclonal selection in TRACERx
- Clonal…
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Hello, Fotakis.
I am using neofuse and I encountered an IndexError during the execution of the script `final_out.py`. The error occurs when the script attempts to access elements in a list that app…
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Run the example data, I receive this error:
python NeoPredPipe.py -I /mnt/bwa-0.7.17/wes/gatk4/gatk-4.0.6.0/0809_somatic.vcf -H /mnt/bwa-0.7.17/output/arcasHLA/arcasHLA/HLA/HRR572954.genotype.json …
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Hello,
Thank you very much for sharing this code!
I would be interested in testing your code on samples other than the ones published in the paper, and I wonder how to create the patients tree…
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From @tavinathanson:
> I'm fairly unclear right now about how best, when using cohorts, to use epidisco results; for example using epidisco neoepitopes rather than https://github.com/hammerlab/cohort…
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Hello,
I have a question regarding the use of normal samples in ScanNeo2.
According to the information provided in the data section of the wiki, it states:
"In addition, normal allows to specif…
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Hello, thank you for developing this useful pipeline!
I have a technical question that I would like to address you.
I noticed from the file file **A5_A3_NetMHC-4.0_junctions_ORF_neoantigens.tab**…
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Hi,
Aplogies if I am sking something pointless I am fairly inexperienced in coding.
I got this error: no such file or directory "assets"
![image](https://github.com/frankligy/SNAF/assets/694271…
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For example:
>>> batch1 = gtex_ctrl_db[:,gtex_ctrl_db.var["tissue"] == "Pituitary"]
>>> batch1
View of AnnData object with n_obs × n_vars = 2476734 × 24
obs: 'mean', 'std'
var: 'tissue', …