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Hi Matt,
I saw from the KPTracer repository that Fitch-Hartigan maximum parsimony can now be calculated in Cassiopeia. Can I calculate the cell-level "scEffectivePlasticity" score in Yang et al…
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Simply ran out of time to get to them in 2018. I have them on a printout.
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There is a slight inefficiency in the sample-optimize-merge loop due to MatOptimize's requirement that all edges have at least one mutation. At present, this is resolved in the following setup:
1. …
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Hi,
I was wondering if the simulated variants* are [normalized](https://genome.sph.umich.edu/wiki/Variant_Normalization) according to the definition of _bcftools_, i.e. are they left-aligned and com…
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Greetings, and thanks for the awesome tool! Is it possible to specify multiple threads? The documentation suggests that Pythia might be able to take advantage of multiple threads, but I cannot see how…
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This is a beginning step toward implementing #6
Since the callback has access to the altered/updated nodes for a given move, we can fully resolve these nodes without using the entire tree if we us…
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@yceh Thanks for fixing a previous issue I was having with this setup! I finally got around to trying out your fix, but I'm now having the following issue. Any ideas?
# Setup:
(on Mac, because the…
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Just to remind myself:
* Make new export_breakpoints() function in the sc2ts main repo. We can, if necessary, incorporate this into export_recombinants. This will only look at the breakpoints in th…
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There may be a lineage circulating in China sampled from travellers from China directed to both Italy and France.
Tree:
![Schermata 2023-01-17 alle 09 26 01](https://user-images.githubuserconten…
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**Submitting author:** @wrightaprilm (April Wright)
**Repository:** https://github.com/wrightaprilm/treesiftr
**Version:** v1.0.0
**Editor:** @juanklopper
**Reviewer:** @ethanwhite, @rachelss
**Archiv…