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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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[database] A double-checked database of Neisseria meningitidis
#267
tanzhizhou
closed
4 months ago
8
visualize only query?
#266
reaset41
closed
7 months ago
1
--write-references option when running PopPUNK assign
#265
avrilcoghlan
closed
7 months ago
2
Retreive source sequences from a database
#264
phisanti
closed
1 year ago
1
Popunk installed with conda cannot import scikit-learn's KernelDensity
#263
sapoudel
closed
1 year ago
0
Check for special characters in sample names
#262
johnlees
opened
1 year ago
0
Fix for using visualise with indiv refine ref-db
#261
johnlees
closed
1 year ago
0
Unmatched parentheses in newick tree
#260
drhoads
closed
1 year ago
12
Iterative PopPUNK updates
#259
BZhao95
closed
1 year ago
1
Query data not working
#258
Drojok
closed
1 year ago
10
Correct database content filenames
#257
HarryHung
closed
1 year ago
0
Increase default mandrake maxiter by 10x
#256
johnlees
closed
1 year ago
0
Increase maxIter with mandrake, and also add option
#255
johnlees
closed
1 year ago
1
Wrong DB for E. coli
#254
jpaganini
closed
1 year ago
2
Can't download Enterococcus faecium databases
#253
martinmchugh
closed
1 year ago
2
Path fix for distance plot, update docs with new DB page
#252
johnlees
closed
1 year ago
0
Updates for GPU analysis + documentation
#251
nickjcroucher
closed
1 year ago
0
Investigate slow assignment with full DBs vs ref DBs
#250
johnlees
opened
1 year ago
0
Replace network code with pp-netlib
#249
johnlees
opened
1 year ago
0
Running Poppunk v2.5.0 with --multi-boundry --> OverflowError
#248
avonm
closed
7 months ago
8
Clustering may not be reproducible with some large data sets
#247
stitam
closed
7 months ago
5
Fix a broken error message in assign
#246
johnlees
closed
1 year ago
0
Proceed with update-db on QC failure
#245
johnlees
closed
1 year ago
0
Remove blas
#244
johnlees
closed
1 year ago
0
Allow update DB with QC failures
#243
johnlees
closed
1 year ago
0
Update and align installation requirements with requirements file.
#242
ccoulombe
opened
1 year ago
2
AttributeError: module 'pp_sketchlib' has no attribute 'sparsifyDists'
#241
drhoads
closed
1 year ago
3
Fix for assign with threshold models
#240
johnlees
closed
1 year ago
0
Fix option names for k-mer range min/max and k-mer step.
#239
tmaklin
closed
1 year ago
1
issue with recent joblib update
#238
jts1044
closed
1 year ago
1
Find BLAS
#237
ccoulombe
closed
1 year ago
2
Patch for relative paths in plot fit
#236
johnlees
closed
1 year ago
0
Using Multiboundary/iterative option
#235
andreaniml
closed
1 year ago
5
Out of memory killer whyle runnin poppunk_visualise
#234
acpaulo
closed
1 year ago
11
Append distance based QC fails to qcreport
#233
jdaeth274
closed
1 year ago
4
Lineage model fitting - PopPUNK changes
#232
nickjcroucher
closed
1 year ago
2
Can't use absolute paths in --create-db (poppunk==2.5.0)
#231
bioinformagica
closed
1 year ago
2
Update with changes to master
#230
nickjcroucher
closed
1 year ago
0
Problem installing latest version in conda - libglib
#228
hmedwards
closed
1 year ago
4
HDBSCAN causing CI to fail
#227
johnlees
closed
1 year ago
1
Adds poppunk_distribute_fit.py
#226
samhorsfield96
closed
1 year ago
0
Microreact crashes
#225
andreaniml
closed
1 year ago
8
Occassional problem with .dot output scale in microreact
#224
johnlees
closed
1 year ago
0
conda install fails
#223
chahatupreti
closed
1 year ago
2
Cytoscape visualisation with queries not showing all edges
#222
johnlees
opened
1 year ago
0
creating database step gives error
#221
danrlu
closed
1 year ago
4
Fit a dbscan model with 7 Clusters But visualise's result has more than 7 Clusters
#220
shaodongyan
closed
1 year ago
2
poppunk_visualise failed
#219
shaodongyan
closed
1 year ago
6
increase the version in __init__.py
#218
BZhao95
closed
1 year ago
1
Small fixes for beebop
#217
muppi1993
closed
1 year ago
0
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