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@jjgao commented on [Fri Dec 22 2017](https://github.com/cBioPortal/GSoC/issues/40)
**Background**:
Signatures of mutational processes in human cancers can be inferred from somatic mutations data…
jjgao updated
4 years ago
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> ... transcription factor motif analysis was carried out with the FIMO package, with a p-value threshold of 0.001. A total of 614 human transcription factor binding motifs from the HOCOMOCO database …
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- [x] Methylation tab cBioPortal/cbioportal#7683
- [ ] Should we support continuous CNA data?
- [x] Support patient level enrichments analysis cBioPortal/cbioportal#4637
- [x] treat overlapping pa…
jjgao updated
7 months ago
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**Is your feature request related to a problem? Please describe.**
Stryker run mutations with dubious coverage info against all tests. This is a logical defensive measure, but it can be a problem whe…
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Hello CRISPResso Team -
I am currently using the CRISPRessoWGS feature to quantify editing of CRISPR treated samples with 2 sgRNAs. These cut sites are close in proximity - 4 bases apart to be prec…
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I'm wondering if it would be appropriate to add functionality of reading files such as [`simple_somatic_mutation.open.BRCA-US.tsv.gz`](https://dcc.icgc.org/releases/release_17/Projects/BRCA-US).
Re…
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Hello,
I notice that you did phylogenetic trees in CITUP with the output from PyClone.
However, In my work, run_analysis_pipeline commands can't give an output of mutations which didn't appear in …
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Sometimes a few tests exist that fail during the initial coverage analysis for whatever reason (e.g., caused by the class loading), although, they succeed when executed with `mvn verify`.
However, th…
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@jbloom one of the reviewers had the following comment:
_Different methods might exhibit various efficiencies for predicting mutations on different regions of the Spike. Is it possible to analyze t…
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The Hands-On tutorial in the "Mapping and molecular identification of phenotype-causing mutations" in the Variant Analysis Section needs Some clarity on assumptions such as recessive mutation and the …