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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 python 3.10 and 3.11 support
#251
colganwi
opened
5 days ago
1
v4 chemistry
#250
diazlab
opened
1 month ago
3
Call lineages questions
#249
JReneCWong
closed
1 month ago
3
How to write to a newick tree with root?
#248
teng-gao
opened
1 month ago
1
IndexError: list index out of range
#247
teng-gao
closed
1 month ago
2
Segmentation fault in cas.pp.align_sequences
#246
peipp410
opened
3 months ago
0
Fitness estimation not included on readthedocs
#245
colganwi
opened
3 months ago
0
Does Cassiopeia have the Function to directly get fitness score?
#244
tenlives
closed
3 months ago
9
"Aborted (core dumped)" during the align step in cassiopeia-preprocess
#243
sk7944
closed
3 months ago
2
CCPhylo branch lengths
#242
colganwi
opened
5 months ago
0
#cassiopeia.pl.plot_matplotlib() failed to add meta_data information
#241
jinyongfan
closed
5 months ago
2
ecDNA simulator
#240
mattjones315
closed
5 months ago
3
ILPSolverError: Potential Graph could not be found with solver parameters.
#239
tenlives
closed
7 months ago
4
Lca reconstruct
#238
mattjones315
closed
7 months ago
1
Potential Bug in intBC extract
#237
jefferyUstc
opened
8 months ago
1
How to use Cassiopia to analyze bulk DNA sequencing data
#236
yuangh16
closed
7 months ago
1
sped up average missing data
#235
mattjones315
closed
8 months ago
1
“Error” in function `error_correct_intbcs_to_whitelist`
#234
jefferyUstc
opened
10 months ago
0
Single thread hybrid solver
#233
colganwi
closed
8 months ago
3
Newick string branch length support
#232
colganwi
closed
9 months ago
1
Computing tree likelihoods
#231
Marius1311
opened
1 year ago
0
Colors in `cassiopeia.pl.plot_matplotlib` not reproducible
#230
Marius1311
closed
7 months ago
7
Sequential lineage tracing data simulator
#229
colganwi
closed
8 months ago
1
Leaf Subsampler Speedup
#228
colganwi
closed
1 year ago
2
fixed cmap bug created by pr:182
#227
colganwi
closed
1 year ago
0
Ambiguous greedy & parallel dissimilarity computation
#226
mattjones315
closed
1 year ago
2
Improved doublet detection in `call_lineages`
#225
colganwi
opened
1 year ago
0
Parameter tuning for the hybrid solver
#224
Marius1311
closed
1 year ago
2
Update README.md
#223
mattjones315
closed
1 year ago
0
how to display cutsite name in cas.pl.plot_matplotlib
#222
tenlives
closed
1 year ago
1
Update documentation
#221
mattjones315
closed
1 year ago
1
Clean fix dtype checking in local plotting
#220
colganwi
closed
1 year ago
1
Example `reorder_children` in plotting tutorial
#219
mattjones315
opened
1 year ago
0
Check whether the ILP Solver is using Gurobi
#218
Marius1311
closed
1 year ago
2
Reorder children in tree
#217
colganwi
closed
1 year ago
3
Generalization of Cas9LineageTracingDataSimulator
#216
colganwi
closed
1 year ago
1
Spatial leaf subsampler
#215
colganwi
closed
1 year ago
1
Refactor `solver` module
#214
mattjones315
opened
1 year ago
0
ILP solver failing
#213
Marius1311
closed
1 year ago
2
Neighbor-Joining algorithm using weighted Hamming distance
#212
YushaLiu
closed
1 year ago
2
CRISPR-Cas9 distance correction solver
#211
sprillo
opened
1 year ago
3
Calculate cell level plasticity score
#210
YushaLiu
closed
1 year ago
3
How to speed up evolutionary coupling computation
#209
Marius1311
closed
1 year ago
4
Added spatial leaf subsampler
#208
colganwi
closed
1 year ago
0
Fixed ILP cython error caused by pandas update
#207
colganwi
closed
1 year ago
1
Regular scRNA-seq data as only input for Cassiopeia
#206
ioyarzun
closed
1 year ago
2
Fast UPGMA and NJ with CCPhylo
#205
colganwi
closed
1 year ago
7
Cassiopeia does not finish after a couple of days
#204
YushaLiu
closed
1 year ago
4
Unable to read pickled files due to renaming of module?
#203
ekmolloy
closed
1 year ago
3
RF and triplets correct should deepcopy
#202
sprillo
closed
1 year ago
1
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