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YosefLab
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Cassiopeia
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
https://cassiopeia-lineage.readthedocs.io/en/latest/
MIT License
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Added character matrix layer functionality
#101
mattjones315
closed
3 years ago
1
Complete binary tree simulator
#100
Lioscro
closed
3 years ago
0
Add functionality in pipeline to create unmapped bam from fastqs (drop cellranger dependency)
#99
Lioscro
closed
3 years ago
0
ILPSolver Potential Graph Speedup & Refactor
#98
mattjones315
closed
3 years ago
1
Supercellular sampler
#97
Lioscro
closed
3 years ago
2
Fix DistanceSolver adding non-unique node names
#96
Lioscro
closed
3 years ago
1
General bd simulator
#95
richardyz98
closed
3 years ago
0
added STDR wrap-around
#94
richardyz98
opened
3 years ago
0
fix character matrix tests when using newer numpy versions
#93
Lioscro
closed
3 years ago
0
test fixes for python 3.8 and newer numpy versions
#92
Lioscro
closed
3 years ago
0
Leaf subsampler border case bug
#91
sprillo
closed
3 years ago
1
remove pathlib from requirements and set python version
#90
Lioscro
closed
3 years ago
0
Update iTOL plotting function + minor fix
#89
Lioscro
closed
3 years ago
0
added critique_old
#88
richardyz98
closed
3 years ago
0
Critique dummy
#87
richardyz98
closed
3 years ago
0
Critique
#86
mattjones315
closed
3 years ago
1
fix sort_cellranger_bam chunked sorting
#85
Lioscro
closed
3 years ago
3
[Don't review] Add UniformCellSubsampler
#84
sprillo
closed
3 years ago
0
[Ready for Review] Add UniformLeafSubsampler and moved collapsing mutationless edges into CassiopeiaTree
#83
richardyz98
closed
3 years ago
0
CassiopeiaTree doesn't trigger error if the character matrix indices don't correspond to tree cells on initialization
#82
richardyz98
closed
3 years ago
1
added branch length to newick generation and itol plotting
#81
richardyz98
closed
3 years ago
0
"to_newick" utility function does not transfer branch lengths
#80
richardyz98
closed
3 years ago
1
PCT48 hardcoded into processing pipeline?
#79
oligomyeggo
closed
3 years ago
3
[Ready for Review] Cas9-based Lineage Tracing Experiment Simulator
#78
mattjones315
closed
3 years ago
3
[Don't Review] Add IIDExponentialLineageTracer
#77
sprillo
closed
3 years ago
0
Ilp bug
#76
mattjones315
closed
3 years ago
0
[Ready for Review] General bd simulator
#75
sprillo
closed
3 years ago
0
Add concrete class TumorWithAFitSubclone that implements a TreeSimulator
#74
sprillo
closed
3 years ago
3
SharedMutationJoiner (UPGMA-like algorithm)
#73
richardyz98
closed
3 years ago
0
Blacked Files
#72
richardyz98
closed
3 years ago
0
blacked files
#71
richardyz98
closed
3 years ago
0
iTOL Plotting Library
#70
mattjones315
closed
3 years ago
2
Add simulation APIs
#69
sprillo
closed
3 years ago
0
New utilities
#68
mattjones315
closed
3 years ago
0
UPGMASolver
#67
richardyz98
closed
3 years ago
0
Quick bugfix
#66
mattjones315
closed
3 years ago
0
[Still Experimental] Ilpsolver logdir
#65
sprillo
closed
3 years ago
1
Move ILPSolver logfile argument from solve() to __init__()
#64
sprillo
closed
3 years ago
1
Quick bugfix
#63
mattjones315
closed
3 years ago
0
Process pipeline richard
#62
richardyz98
closed
3 years ago
0
Solver tree refactor
#61
mattjones315
closed
3 years ago
0
Process pipeline richard
#60
richardyz98
closed
3 years ago
0
Revert "Process pipeline richard"
#59
richardyz98
closed
3 years ago
0
Refactor
#58
richardyz98
closed
3 years ago
0
Hybrid refactor
#57
mattjones315
closed
3 years ago
0
Bugfix: do not expose internals of the CassiopeiaTree
#56
sprillo
closed
3 years ago
0
Remove duplicated code on error raising.
#55
sprillo
closed
3 years ago
0
Minor changes to CassiopeiaTree
#54
mattjones315
closed
3 years ago
0
Fix failing test: Rename mapping => character_state_mapping.keys
#53
sprillo
closed
3 years ago
1
Process pipeline richard
#52
richardyz98
closed
3 years ago
0
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