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This wiki page seems to be missing its contents:
https://github.com/sankaranlab/SCAVENGE/wiki/%5BSCAVENGE-L%5D-Analysis-for-DNA-mutation-based-lineage-tracing
As a side note, you may want to con…
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I would like to discuss potential tools which we can use to keep codebase in good shape.
1. Starting with well know static analysis tools:
- Checkstyle
- Findbugs
- PMD
2. What about covera…
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Hi,
Here's an dummy example of a YAML report generated by mutpy:
```yaml
coverage:
all_nodes: 0
covered_nodes: 0
mutation_score: 90.0
mutations:
- exception_traceback: "Traceback (most…
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https://vatlab.github.io/vat-docs/documentation/vtools_commands/update/
Examples: add genotype info field
```
$ vtools update variant --from_file V*_hg38.vcf --geno_info DP
INFO: Using primary ref…
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We have tried running QA(non-large), document classification and the 3 RE models. All of them seem to have learned1, learned2,.... learned9 in the output.
What do they stand for or is there any step …
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Hi!
I'd liek to try out the scripts, I have two isolates to analyze.
Could you perhaps provide some documentation in terms of the sequence of the scripts. I can more or less figure it out but I'd …
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enzet updated
7 years ago
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Hello,
Thank you for such a useful package! I have two queries:
1. When estimating per-gene dNdSCV ratios and confidence intervals using the geneci function, is it possible to calculate a "combine…
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### Scope - third-party tools integration
The idea is relatively simple: some mutations don't make sense, according to **other** tools that are completely third-party to infection.
Such tools co…
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It would be nice to have an extension to the ChainRules API that allowed for different rules to be written and hit depending on what combination of inputs the derivative is being taken with respect to…