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### Snakemake pipeline steps
**Alignment and quality control**
- [x] align
- [x] fingerprint
- [x] gencode
**Somatic variant calling**
- [x] mutect
- [x] m2db
**Copy number calling**
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We've found that there can be very little variation in expected integration times, see #7 - how do we quantify these times? I think the only alternative is to generate a random sample from these post…
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DLBCL (DOID:0050745) currently has terms for the subgroups that are defined by gene expression analysis. For example, DOID:0080996 and DOID:0080997.
There are now some new entities defined within …
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Does the poltSignatures function have a built in method for labelling individual bars in the resulting barplot with the corresponding trinucleotide context? As in Fig 5a from the Campbell _et al._ _Ce…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/ErasmusMC-CCBC/katdetectr
Confirm the following b…
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https://www.nature.com/articles/s41586-019-1775-1
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this ch…
jjgao updated
2 years ago
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Hi,
Running function combineBCR() is very slow for me, comparing to relatively faster computation for combineTCR(), using the same number of samples and similar data size. I wonder what could be th…
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There are a few reasons this may be a bad approximation:
* the outcome variable is the expected number of substitutions per site (ESS), which is like a transformation of the count outcome (number of …
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# BCR support meta issue.
## Initial PR #183 addresses:
- [x] change datastructure
* Instead of `TRA_1`, `TRA_2`, `TRB_1` and `TRB_2` have `arm1_primary`, `arm1_secondary`, `arm2_primary` an…