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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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Dear Michael,
We have read your paper recently and found it was a very nice idea to predict neoantigen from RNA data. Thank you for your great job!
While we had some problems with our data ana…
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With #754 we're halfway to also supporting inframe indels so we should just do the rest of the work necessary to support those types of proximal variants.
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To build negative sample pairs, we need to make randomly alignment sequence for CDR3 region sequence.
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Hi I have failed docker building process.
Step 11/35 : RUN cd /tmp && wget https://kent.dl.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz && tar xvfz vcftools_0.1.13.tar.gz && cd vcfto…
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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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COVID is not popular anymore and people are switching back to cancer immunotherapy, we must respect our target audience :)
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One thought: ImmPort has a lot of vaccine studies w/ HLA type and RNA-Seq data (maybe some have germline WES?)
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