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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', …
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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, thanks for the fantastic tool!
I have been using it for many years, but I am facing a bug I have never encountered.
I am running Neopredpipe for a set of samples, separating them by SNPs an…
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child of #3
arkal updated
6 years ago
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Hi,
I have run the NeoPredPipe.py as:
`python NeoPredPipe.py -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun -c 1 2 -E 8 9 10`
INFO: Annovar reference files of build h…
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Thank you very much for your excellent work.
I encountered some errors while running my own data following the [tutorial.](https://snaf.readthedocs.io/en/latest/tutorial.html) Here is the error log:…
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1. We don't have a normal sample.. Is it okay to run it without a normal sample?
It generate result file well..
2. Is agretopicity indicates binding affinity?
When I googled it says it's the rati…
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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 have been testing pVAC-seq with a few samples. For each sample, I have typically 150-400 somatic PASS mutations, of which ~40-75 are missense variants. I am using quite a new version of pVACt…