Cassiopeia
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YosefLab
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
Hi, I used ilp Solver on around 20 taxa dataset. The output from ilp Solver is a Digragh. When i try to export it into a newick fomat. Sometimes it...
Thanks for developing such a useful tool for reconstructing phylogenetic tree. when looking into the source code of assigning lineage groups to each cells, I am not sure about if...
This pull request includes the generalization of the `collapse_mutationless_edges` function. This allows us to use a function that does not factor in missing data when determining whether to collapse two...
From the following code snippet, we see that even though the cached edges do not change, the underlying backend networkx object has changed, with the singleton edge at the top...
1. File (module) names should be all lowercase see: https://www.python.org/dev/peps/pep-0008/#package-and-module-names -- and this is causing an issue with autosummary for nice class pages in the docs 2. For an import...
Currently, there is no option to plot indel heatmaps only using the character matrix. As of now, the full allele table is required. Extend the plotting functionality to support this...
Implement utilities from recent [KP-Tracer manuscript](https://www.biorxiv.org/content/10.1101/2021.10.12.464111v1) into the Cassiopeia codebase. Specifically: - Expansion index - Phylogenetic coupling - Phylotime
Make an argument `use_priors` in `CassiopeiaSolvers` that dictates whether or not to use priors during reconstruction of a tree. The current behavior is that if priors exist within a `CassiopeiaTree`,...
Should be a simple fix, but just posting as an issue so that we get to it some time. We should unify local importing to use relative imports (i.e. `from...
Currently we are invoking `copy.deepcopy(self)` when trying to copy a CassiopeiaTree. It would be better to implement a custom version of both `copy` and `deepcopy` for users. See https://docs.python.org/3/library/copy.html ,...