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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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Update poppunk_iterate.py
#216
BZhao95
closed
1 year ago
0
Read the docs sphinx version
#215
johnlees
closed
1 year ago
0
HDBSCAN models require consistent version of sklearn to open
#213
victoriapascal
closed
1 year ago
16
Add rapidnj to docker image
#212
muppi1993
closed
1 year ago
0
Error install Poppunk
#211
OrsonMM
closed
1 year ago
3
OSError when running poppunk_visualise with cytoscape even in emulated osx-64
#210
acpaulo
closed
1 year ago
16
pip installable poppunk, almost
#209
richfitz
closed
1 year ago
2
pip installable poppunk, almost
#208
richfitz
closed
2 years ago
1
--prop-n flag and ambiguous bases
#207
jennahamlin
closed
1 year ago
4
Integrate changes from V250 candidate
#206
nickjcroucher
closed
2 years ago
0
Update with recent changes to master
#205
nickjcroucher
closed
2 years ago
0
Release for v2.5.0
#204
johnlees
closed
1 year ago
9
Replace dendropy
#203
johnlees
closed
1 year ago
0
New logo
#202
johnlees
closed
1 year ago
0
Bacpop 17
#201
muppi1993
closed
2 years ago
4
Using PopPunk for plasmids
#200
andreaniml
closed
2 years ago
1
Multiple genome files reported to contain no sequence
#199
drhoads
closed
2 years ago
4
poppunk 2.4.0: sklearn version not compatible with poppunk
#198
nicola-palmieri
closed
2 years ago
3
Clusters.csv reports all samples belong to the same cluster
#197
VishnuRaghuram94
closed
2 years ago
6
Subsetting the database when using poppunk_visualise --cytoscape with --include-files
#196
muppi1993
closed
1 year ago
5
Update parsing fixes branch with new master
#195
nickjcroucher
closed
2 years ago
0
All clusters merged into a single one when trying to assign new strains
#194
flass
closed
1 year ago
7
Help with issues running poppunk in HPC environment
#193
CarmenSheppard
opened
2 years ago
8
Lineage clustering - how to evaluate results
#192
andreaniml
closed
2 years ago
2
Documentation update
#191
johnlees
closed
1 year ago
0
Give clearer results when queries are in the reference DB
#190
johnlees
closed
1 year ago
2
Update documentation for assign + lineage mode
#189
johnlees
closed
1 year ago
0
Unable to run poppunk_assign or --fit-model on E. coli database
#188
matnguyen
closed
2 years ago
2
Unrecognized arguments in poppunk_assign: --assign-lineages and --rank
#187
ChadFibke
closed
2 years ago
3
fit-model RecursionError
#186
ChadFibke
closed
2 years ago
3
Update tutorial with new Cytoscape command
#185
nickjcroucher
closed
1 year ago
0
Cytoscape visualization not being generated
#184
andreaniml
closed
2 years ago
4
Problem fitting Salmonella Typhimurium database- convergence error
#183
andreaniml
closed
2 years ago
2
Issues with refine - RuntimeError: Optimisation failed: produced a boundary outside of allowed range
#182
bananabenana
closed
2 years ago
3
Error generating tuples in distance QC
#181
jdaeth274
closed
2 years ago
2
Multi-boundary method
#180
johnlees
closed
2 years ago
0
poppunk_visualise failed to parse a long path to the model directory
#179
wanyuac
closed
2 years ago
3
Move the extend algorithm into the C++ extension
#178
johnlees
closed
2 years ago
2
Update MST calculation documentation
#177
nickjcroucher
closed
2 years ago
0
Problem in assigning lineages - poppunk_assign crashing
#176
andreaniml
closed
2 years ago
3
Upgrades to refinement functions
#175
nickjcroucher
closed
2 years ago
16
Give a 'scaled' option for manual start
#174
johnlees
closed
1 year ago
0
Error running rapidnj in poppunk_visualize
#173
drhoads
closed
3 years ago
3
terminate called after throwing an instance of 'std::runtrime_error'
#172
drhoads
closed
3 years ago
4
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
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