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I am wondering if there is any documentation of how to use regexner and TokensRegex annotators in Python wrapper of corenlp. And also, how can I use my own customised regular expression?
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@cjllanwarne helped me with this issue but its led to new ones:
https://github.com/broadinstitute/cromwell/issues/5793
Cromwell tries to chmod the mounted sra directory which is not allowed.
cod…
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Hi Daniel,
i have noticed the same issue in version 1.33 for IGH@ locus and MYC.
Could you please have a look at it? Thank you.
### IGH@
chr14:105,556,000-106,883,700 (hg38 location)
FusionCatc…
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Survival analysis (Cox regression and ggforest plot)
- 25 different tumors and no cancers
- PTV burden as a continuous variable
- Variables in the Cox models: sex, ethnic group, PCA1-10, PTV burd…
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Hi,
I am very interesting in your VisualMSI tool, since it is quite simple to use and very fast to find the microsatellites.
However, I am confusing how to determine the MSI status, etc. MSS, MS…
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https://doi.org/10.1158/2159-8290.CD-22-0196
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this check…
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https://www.nature.com/articles/s41586-022-05068-3
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this c…
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https://www.nature.com/articles/s41588-022-01159-z
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this c…
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I noticed that the VCFs produced by VarDict include `AF` in the `FORMAT` as well as `INFO` sections: https://github.com/AstraZeneca-NGS/VarDict/blob/master/var2vcf_paired.pl#L50
I guess this is tec…
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https://pubmed.ncbi.nlm.nih.gov/34715028/
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this checklist …