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bacpop
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PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
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AttributeError when refining a model
#171
mgalardini
closed
3 years ago
3
Existing database cannot be in nested directories
#170
mgalardini
closed
3 years ago
6
cannot import name 'gcd' from 'fractions'
#169
cizydorczyk
closed
2 years ago
4
Remove start_point concept from refine fit
#168
johnlees
closed
3 years ago
2
Poppunk ValueError (sklearn) when generating database
#167
BioMinnie
closed
3 years ago
7
Remove dbFuncs dictionary
#166
johnlees
opened
3 years ago
0
Upgrade of GPU refinement
#164
nickjcroucher
closed
3 years ago
3
NOTE: NTP898 required densification ?
#163
dineshkumarsrk
closed
3 years ago
2
Turn off docker builds on tags
#162
johnlees
closed
3 years ago
0
Add alternate names, method description
#161
johnlees
closed
3 years ago
0
Fix older scripts
#160
johnlees
closed
3 years ago
0
genome name changed in output NJ_tree
#159
flass
closed
3 years ago
6
FileNotFoundError when writing plot fits
#158
flass
closed
3 years ago
4
AttributeError: 'numpy.uint64' object has no attribute 'out_edges'
#157
flass
closed
3 years ago
2
AttributeError: module 'pp_sketchlib' has no attribute 'assignThreshold'
#156
dineshkumarsrk
closed
3 years ago
3
DBSCAN and BGMM assignment improvements
#155
johnlees
closed
3 years ago
0
Parallelise assignment
#154
johnlees
closed
3 years ago
0
Add alternative strain names
#153
johnlees
closed
3 years ago
1
Label order
#152
nickjcroucher
closed
3 years ago
0
Don't try and make trees with fewer than three samples
#151
johnlees
closed
3 years ago
0
Update MST branch with fixes to iterative querying
#150
nickjcroucher
closed
3 years ago
0
Update random when assign uses update DB
#149
johnlees
closed
3 years ago
0
Updates to MST
#148
nickjcroucher
closed
3 years ago
3
Move C++ network code from sketchlib into PopPUNK
#147
johnlees
closed
3 years ago
0
Add alternative network scores
#146
johnlees
closed
3 years ago
4
MST improvements
#145
johnlees
closed
3 years ago
0
Update MST branch with changes to master
#144
nickjcroucher
closed
3 years ago
1
ModuleNotFoundError: No module named 'sklearn.neighbors.kde'
#143
samlipworth
closed
3 years ago
4
AttributeError in reference clique pruning
#142
dsurujon
closed
3 years ago
7
Add calculation of minimum spanning trees
#141
nickjcroucher
closed
3 years ago
4
Specify dendropy version
#140
johnlees
closed
3 years ago
0
Specify rapidnj's threads
#139
johnlees
closed
3 years ago
0
Update issue templates
#138
johnlees
closed
3 years ago
0
Fix to QC function
#137
nickjcroucher
closed
3 years ago
3
Plot fit update
#136
nickjcroucher
closed
3 years ago
2
Accessory distance issue
#135
sbberes
closed
3 years ago
22
Fix duplication of names in QC function
#134
nickjcroucher
closed
3 years ago
0
Add dockerization of API
#133
johnlees
closed
3 years ago
0
Attempt to fix readthedocs builds
#132
johnlees
closed
3 years ago
0
Web
#131
Danderson123
closed
3 years ago
0
Improve distance estimation
#130
nickjcroucher
opened
3 years ago
2
Save the full distance matrix with assign
#129
johnlees
closed
3 years ago
0
Assign with update DB only saves ref distances
#128
johnlees
closed
3 years ago
0
Illegal instruction (core dumped) when running PopPUNK
#127
dmgie
closed
3 years ago
20
New network score
#126
johnlees
closed
3 years ago
0
Update CLI defaults to be simpler
#125
johnlees
closed
3 years ago
0
Web
#124
Danderson123
closed
3 years ago
0
Add option to save distances as edge weights in graph
#123
johnlees
closed
3 years ago
0
Update documentation to reflect new API (v2.3.0)
#122
johnlees
closed
3 years ago
0
Add lengths to network edges for visualisation
#121
johnlees
closed
3 years ago
3
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