Cassiopeia
Cassiopeia copied to clipboard
YosefLab
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
This PR changes the behavior of the CCPhylo based solvers. Instead of setting all branch lengths to 1 it uses the branch lengths output by CCPhylo.
Hi, i have a problem on the make test step in the Installation. And i have tried some methods mentioned online and failed , and i wonder why this package...
Hi Cassiopeia Team, I carefully checked the result from [Cassiopeia](https://github.com/YosefLab/Cassiopeia), and Found a bug in some reads in `SRR11357694`, for example: `AATCCAGCTAGCTGTGCAGCTCTCCGTTAGACATTTCAACTGCAGTAATGCTACCTCGTACTCACGCTTTCCAAGTGCTTGGCGTCGCATCTCGGTCCTTTGTACGCCGAAAAATGGCCTGACAACTAAGCTACGGCACGCTGCCATGTTGGGTCATAACGTGGTTCATCCGTGACCGAACATGTCATGGAGTAGCAGGAGCTATTAATTCGCGGAGGACAATGCGGTTCGTAGTCACTGTCTTCCGCAATCGTCCATCGCTCCTGCAGGTGGCCTAGAGGGCCC` with CIGAR(34M1D127M7D124M), we could manually map this to...
This PR makes a number of improvements to `call_lineages` step of the preprocessing pipeline. These changes are based on my experience processing a dataset with high ambient RNA and a...
https://github.com/YosefLab/Cassiopeia/blob/2ca07df5a682cd159d4c2119458049b44507eb59/cassiopeia/preprocess/pipeline.py#L686 Hi, Cassiopeia team, is the referenced code above should be corrected to `corrections = {intbc: intbc for intbc in unique_intbcs} ` Thanks!
Hi Cassiopeia team, I was wondering whether there would be a place in the documentation where I can find more information about the computation of tree likelihoods in Cassiopeia? For...
We should have a little example demonstrating how `CassiopeiaTree.reorder_children` can be used to optimize plotting visuals in our plotting tutorial. Mentioned in the discussion around #217.
Implement distance correction scheme for the CRISPR-Cas9 model. The class implementing this method is `CRISPRCas9DistanceCorrectionSolver` in the `cassiopeia/solver/distance_correction/_crispr_cas9_distance_correction_solver.py` module. (The `distance_correction` subpackage is meant to contain any distance correction methods...
Per a recent conversation in issue #205, we've determined that our recent software development efforts have outstripped the implementation of the `DistanceSolver` class. Namely, it's become apparent that the inheritance...
When creating a wrapper around a dissimilarity function from `cas.solver.dissimilarity` and applying it to a `DistanceSolver`'s `dissimilarity_function` argument, I get a numba error. In order to recreate the issue, I...
