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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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Optional Priors Usage in Reconstruction
#151
mattjones315
opened
3 years ago
0
[Ready for Review] Expansion probabilities
#150
mattjones315
closed
3 years ago
4
Implement Utilities from KP-Tracer MS
#149
mattjones315
opened
3 years ago
0
Morans I
#148
mattjones315
closed
3 years ago
3
pass read header to cluster function
#147
Lioscro
closed
3 years ago
1
Precompute dissimilarity map row sums
#146
sprillo
closed
3 years ago
1
Parsimony and likelihood
#145
richardyz98
closed
2 years ago
4
AttributeError calling cassiopeia.pp.align_sequences
#144
oligomyeggo
closed
2 years ago
5
Preprocessing speedup
#143
Lioscro
closed
3 years ago
2
global alignment
#142
Lioscro
closed
3 years ago
1
Bulk remove leaf
#141
richardyz98
closed
3 years ago
1
ILPSolverError when Potential Graph cannot be inferred
#140
mattjones315
closed
3 years ago
1
Deal with empty target site alleles appropriately
#139
Lioscro
closed
3 years ago
1
Cleanup pandas operations in preprocessing pipeline
#138
Lioscro
closed
3 years ago
0
Cleanup filtering code and behavior in preprocess
#137
Lioscro
closed
3 years ago
1
Missing data
#136
oligomyeggo
closed
3 years ago
20
Fix clerical issues
#135
richardyz98
closed
3 years ago
2
Branch length estimation bayesian
#134
sprillo
closed
3 years ago
2
Minor changes to preprocessing utilities
#133
mattjones315
closed
3 years ago
1
Ilp post processing fix
#132
richardyz98
closed
3 years ago
1
Issues with ILP solution post-processing
#131
richardyz98
closed
3 years ago
0
Implement custom copy & deepcopy methods in CassiopeiaTree
#130
mattjones315
opened
3 years ago
0
SpatialSampler
#129
Lioscro
closed
2 years ago
2
unify importing in codebase
#128
Lioscro
opened
3 years ago
0
Global Alignment in Cassiopeia Preprocessing
#127
mattjones315
closed
3 years ago
2
Issue loading in previously saved allele_table
#126
oligomyeggo
closed
3 years ago
7
FitchCount
#125
mattjones315
closed
3 years ago
3
Branch length estimation: MLE
#124
sprillo
closed
3 years ago
4
BrownianSpatialDataSimulator
#123
Lioscro
closed
3 years ago
1
Score character-parsimony and likelihood.
#122
mattjones315
closed
2 years ago
0
Update README.md
#121
richardyz98
closed
3 years ago
0
Merging in refactor
#120
mattjones315
closed
3 years ago
0
Ilp hybrid fixes
#119
richardyz98
closed
3 years ago
0
reconstruct-lineage error: IndexError: index 2 is out of bounds for axis 0 with size 2
#118
isshamie
closed
3 years ago
7
Small Parsimony
#117
mattjones315
closed
3 years ago
2
Test deployment
#116
mattjones315
closed
3 years ago
2
ILPSolver internal nodes naming convention prevents the trees from being converted to newick format
#115
richardyz98
closed
3 years ago
1
DistanceSolver duplicates handling is inconsistent with other solvers
#114
richardyz98
closed
3 years ago
1
Hybrid Solver: logging for the bottom_solver does not work as intended
#113
richardyz98
closed
3 years ago
1
CassiopeiaTree character matrix has inconsistencies in the naming conventions
#112
richardyz98
closed
3 years ago
1
Collapsing
#111
richardyz98
closed
3 years ago
2
Key error when calling cassiopeia.pp.call_lineage_groups
#110
oligomyeggo
closed
3 years ago
22
'cassiopeia' has no attribute 'pp'
#109
oligomyeggo
closed
3 years ago
2
Logging improvements
#108
Lioscro
closed
3 years ago
0
Failed to install
#107
xliu-uth
closed
3 years ago
2
preprocessing pipeline improvements
#106
Lioscro
closed
3 years ago
0
bayesian consensus calling implementation
#105
Lioscro
closed
3 years ago
0
intbc correction to whitelist in preprocessing pipeline
#104
Lioscro
closed
3 years ago
1
add normalized branch length to complete binary simulator
#103
Lioscro
closed
3 years ago
0
Add option to turn off site collapsing in cas9 simulator
#102
Lioscro
closed
3 years ago
0
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