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Clinical-Genomics-Lund
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bonsai
Visualize and analyze resistance and outbreak of bacterial pathogen
https://bonsai-wgs.readthedocs.io/en/latest/
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Entrypoint for adding custom metadata to samples
#124
mhkc
opened
8 months ago
0
Add option for users to reject or pass called resistance genes and variants
#123
mhkc
closed
6 months ago
0
Add SNP clustering
#122
mhkc
opened
8 months ago
0
Add IGV visualization for predicted variants
#121
mhkc
closed
6 months ago
0
Add card for lineages
#120
mhkc
closed
7 months ago
0
Add Mykrobe and TBprofiler AMR cards
#119
mhkc
closed
7 months ago
0
114 remove old project name from grapetree header
#118
mhkc
closed
8 months ago
0
Move output parsers to Bonsai
#117
mhkc
opened
8 months ago
0
Upload script takes yaml file with file paths as input
#116
mhkc
opened
8 months ago
0
Removed old project name from GrapeTree header
#115
mhkc
closed
8 months ago
0
Remove old project name from GrapeTree header
#114
mhkc
closed
8 months ago
0
Labels missing in grapetree
#113
LordRust
closed
8 months ago
0
Fixed resistance_report view crash
#112
mhkc
closed
8 months ago
0
Fix grapetree metadata
#111
mhkc
closed
8 months ago
0
Updates to edit group view
#110
mhkc
closed
8 months ago
2
Release v0.1.0
#109
mhkc
closed
8 months ago
8
Use input data models from JASEN PRP
#108
mhkc
closed
9 months ago
0
Use input data models from JASEN PRP
#107
mhkc
closed
9 months ago
0
Let users set QC status for multiple samples from /groups
#106
alkc
closed
9 months ago
2
99 remove n noel cgmlst alleles from frontend
#105
mhkc
closed
10 months ago
0
Add kraken2 species prediction results to sample view and fix cmlst missing alleles
#104
mhkc
closed
10 months ago
0
Add JSDoc
#103
mhkc
opened
10 months ago
0
User menu dropdown needs solid backgroun
#102
mhkc
closed
9 months ago
0
Add kraken2 species prediction results to sample view
#101
mhkc
closed
10 months ago
0
Number of missing cgmlst loci is not correct
#100
mhkc
closed
10 months ago
0
Remove N noel cgmlst alleles from frontend
#99
mhkc
closed
10 months ago
0
Improve performance of finding and clustering samples
#98
mhkc
closed
10 months ago
15
Bulk mark samples that passed or failed QC
#97
mhkc
closed
9 months ago
4
Resistance gene names are not properly formatted
#96
mhkc
closed
6 months ago
0
Find all samples with a given mutation or arg
#95
mhkc
opened
11 months ago
0
Add more metadata to the sample table
#94
mhkc
closed
3 days ago
0
Accessing resistance report link from sample page triggers an internal server error
#93
alkc
closed
8 months ago
0
Missing cgMLST QC data?
#92
mhkc
closed
9 months ago
0
Load samples to bonsai is very slow
#91
mhkc
closed
10 months ago
0
Find similar samples doesnt scale well
#90
mhkc
closed
10 months ago
0
User accounts do not have permission to add comment and classify QC
#89
mhkc
closed
8 months ago
0
WIP - Build and publish docker images on push/pull to master
#88
alkc
closed
4 months ago
1
/groups/edit: Make it easier to fill in the datatypes and JSON paths inputs
#87
alkc
closed
8 months ago
0
/groups/edit: Make update/delete buttons easier to access
#86
alkc
closed
8 months ago
0
11 document how to release and develop bonsai
#85
mhkc
closed
11 months ago
0
Create group with selected samples
#84
mhkc
closed
4 days ago
1
Add API route for searching for sample using sample ids
#83
mhkc
closed
11 months ago
12
added no groups text if there are no groups
#82
mhkc
closed
11 months ago
0
Groups with more than 500 samples crashes page
#81
mhkc
closed
11 months ago
0
Internal server error `requests.exceptions.HTTPError: 414 Client Error: Request-URI Too Long for url` when trying to cluster large quantity of samples from basket
#80
alkc
closed
11 months ago
2
Fix shifting table rows when applying search filters in /groups
#79
alkc
closed
11 months ago
0
added workaround for $getField
#78
mhkc
closed
11 months ago
0
Fixed signature permission error message
#77
mhkc
closed
11 months ago
0
Include SCRIPT_ROOT in URL creattion w JS
#76
mhkc
closed
11 months ago
1
unsupported operator in sample summary pipeline crashes both api and client
#75
alkc
closed
11 months ago
0
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