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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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Update README.md
#201
mattjones315
closed
1 year ago
0
Show legend for colorstrip when using cassiopeia.pl.plot_matplotlib
#200
YushaLiu
closed
1 year ago
1
Update for Pandas>2.0.0
#199
mattjones315
closed
1 year ago
1
Segmentation Fault in error_correct_cellbcs_to_whitelist
#198
syntonym
closed
1 year ago
5
converted str-> Path during iTOL plotting
#197
mattjones315
closed
1 year ago
1
Allow scaling the tree to an arbitrary depth
#196
sprillo
closed
1 year ago
0
Allow preserving unifurcations when subsampling; write tests
#195
sprillo
closed
1 year ago
0
Allow for double-resection alleles in simulator
#194
sprillo
closed
1 year ago
0
Possible bug in `cas.pl.upload_and_export_itol`
#193
tzeitim
closed
1 year ago
6
Implement vectorized log-likelihood computation to speed up cvxpy.
#192
sprillo
closed
1 year ago
1
How many intBCs are in the intbc_whitelist?
#191
lamyankin
closed
1 year ago
2
Add LBIJungle
#190
sprillo
closed
1 year ago
3
fixed matplotlib plotting bugs
#189
mattjones315
closed
1 year ago
0
results produced by ilp_solver
#188
ask-more-questions
opened
1 year ago
5
issues about assign_lineage_groups() function
#187
AmoriLi
opened
1 year ago
0
ERROR in align
#186
cxyzju
closed
1 year ago
1
Converting FASTQs into an unmapped BAM: Index out of range
#185
george-butler
closed
2 years ago
3
Site rate variation for branch length estimation
#184
scimind1729
closed
2 years ago
1
make test error
#183
ask-more-questions
opened
2 years ago
8
Spatial tree plotting
#182
Lioscro
closed
1 year ago
5
Generalizing 'collapse_mutationless_edges' and small fitchcount bugfix
#181
richardyz98
opened
2 years ago
1
speed up compute_dissimilarity_map
#180
Lioscro
closed
1 year ago
1
Failed Numbaization of Distance Function is Not Caught
#179
ivalexander13
opened
2 years ago
1
pip in Makefile
#178
svenmh
closed
2 years ago
1
refactored how hybrid log files are created
#177
mattjones315
closed
2 years ago
1
Update README.md installation
#176
adamgayoso
closed
2 years ago
1
Update name to cassiopeia-lineage
#175
adamgayoso
closed
2 years ago
2
Error in resolve_umi_sequence
#174
cnk113
closed
1 year ago
5
Triplets Correct and RF functions both mutate the underlying tree
#173
richardyz98
opened
2 years ago
0
File names, import issues
#172
adamgayoso
opened
2 years ago
0
Installation instructions in readme
#171
adamgayoso
closed
2 years ago
1
Infrastructue overhaul
#170
adamgayoso
closed
2 years ago
3
Add utility function to resolve ambiguities in final allele table
#169
Lioscro
closed
2 years ago
1
Fix incorrect umi count displayed in error_correct_umis
#168
Lioscro
closed
2 years ago
1
Fix dtype checking in local plotting
#167
Lioscro
closed
1 year ago
2
Fix dtype checks in local plotting
#166
Lioscro
closed
2 years ago
1
Target site reference fasta in the Science article "Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts"
#165
gloriafight
closed
2 years ago
1
Bam group by speedup
#164
Lioscro
closed
1 year ago
4
remove logging message in error_correct_intbcs
#163
Lioscro
closed
2 years ago
1
change numpy requirement in pyproject.toml to use oldest-supported-numpy
#162
Lioscro
closed
2 years ago
2
SNJ Solver Implementation
#161
kevinan1
closed
2 years ago
1
Support character matrix colorstrips in plotting
#160
Lioscro
opened
2 years ago
0
local plotting
#159
Lioscro
closed
2 years ago
4
SNJ Implementation Draft
#158
ivalexander13
closed
2 years ago
2
understanding the character matrix
#157
ShouWenWang
closed
2 years ago
4
Missing ~/.itolconfig
#156
ShouWenWang
closed
2 years ago
6
Command line tools not found
#155
ShouWenWang
closed
2 years ago
3
Evolutionary coupling
#154
mattjones315
closed
2 years ago
1
Cophenetic Correlations
#153
mattjones315
closed
3 years ago
2
Cophenetic Distance
#152
mattjones315
closed
3 years ago
0
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