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Hello.
I was looking for a workflow for neoantigen prediction and found your great project.
I clicked the link below to see your website, but I couldn't open the page
Parhaps the link may have…
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For the public app, the row order of the heatmap in the Correlations section of “Immune Feature Trends” has changed. It had previously been ordered in a specified way, to be consistent with a manuscri…
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See https://github.com/taylor-lab/neoantigen-dev/issues/8
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Because of the preceding "citations" column 220 containing `#` which was used as `comment=#` in below line of code, column 221 and beyond were truncated causing missing important columns including `Ho…
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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…
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Related to the following: https://hub.docker.com/r/cmopipeline/netmhc
https://github.com/mskcc/vaporware/pull/314
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```
/usr/local/bin/neoantigen/neoantigen.py:247: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. DONE
maf_df = pd.read_table(maf_file, comment='#', low_memory=Fals…
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Lots of people use nf-core pipelines offline. We want to make the process of using modules from a different repository as simple as possible.
One solution would be to use `git submodule` to add `nf…
ewels updated
4 years ago
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We should do this with some due diligence to make sure we're not throwing important stuff away:
Barry wrote
"""
Deleting from current output that are not mentioned above:
• somatic_variants/de…
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Below two lines result in duplicated level of neoantigen directory in the "Result" folder when publishing the result
https://github.com/mskcc/vaporware/blob/bfc446dc16336802790e6644f37e1e9f0cc32fd8…