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artic-network
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civet
Cluster Investigation & Virus Epidemiology Tool
https://cov-lineages.org/resources/civet.html
GNU General Public License v3.0
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Additional setup dependency for jupyter-client
#115
matt-sd-watson
closed
3 years ago
2
Speed up for background fasta file parsing- don't use biopython
#114
aineniamh
opened
3 years ago
0
remove max memory
#113
aineniamh
closed
3 years ago
1
private columns as env variable, public flag for safe report
#112
aineniamh
opened
3 years ago
0
Maximum tree size to build, else pass and just show summary.
#111
aineniamh
closed
3 years ago
1
Add configurable tree annotations in report
#110
aineniamh
closed
3 years ago
1
Negative Dimensions Not Allowed
#109
mattloose
closed
3 years ago
2
full pipeline description docs
#108
aineniamh
opened
3 years ago
0
Feature: infer local catchment phylotypes
#107
aineniamh
opened
3 years ago
0
Random downsampling issue of some sort
#106
aineniamh
closed
3 years ago
6
Identical IDs get collapsed in all but timeline (and that functionality wants to stay the same)
#105
ViralVerity
closed
3 years ago
1
identical sequences not shown in snipit
#104
aineniamh
closed
3 years ago
0
Custom report headers and footers
#103
rambaut
opened
3 years ago
0
Option to annotate with specified SNPs
#102
rambaut
closed
3 years ago
1
Allow export of figures/data from reports
#101
rambaut
closed
3 years ago
2
Suggestion for option to generate config file and stop
#100
rambaut
opened
3 years ago
0
Feature Request: Export SNIPIT
#99
mattloose
closed
3 years ago
4
Fix installation versioning issues in both conda yml and setup.py
#98
matt-sd-watson
closed
3 years ago
0
Is this tool at production stage?
#97
domenico-simone
opened
3 years ago
3
Install error
#96
BioWilko
closed
3 years ago
0
PR cog-uk civet to artic civet
#95
aineniamh
closed
3 years ago
0
Add more to example report
#94
ViralVerity
opened
3 years ago
1
Manual improvement
#93
josephhughes
closed
3 years ago
1
Make hide cog-ids in table an optiono
#92
ViralVerity
opened
3 years ago
0
too big tree something or other
#91
aineniamh
closed
3 years ago
0
Actions dev
#90
ViralVerity
closed
3 years ago
0
Make tree figures optional in report
#89
ViralVerity
closed
3 years ago
0
Add a summary "summarise lineage by" type option to make a context table
#88
ViralVerity
closed
3 years ago
0
delete old file"
#87
ViralVerity
closed
3 years ago
0
fix broken map link
#86
ViralVerity
closed
3 years ago
0
Clean adm2s
#85
ViralVerity
closed
3 years ago
0
if no adm2 information in background, will get flagged as old_data (pre clean adm2 in grapevine) and so won't map ambiguous locations given in input csv
#84
ViralVerity
opened
3 years ago
1
Make background map files configurable
#83
ViralVerity
closed
3 years ago
0
Upstream/artic dev
#82
aineniamh
closed
3 years ago
0
Summarise collapsed nodes - should they be on the tree at all?
#81
ViralVerity
closed
3 years ago
0
Anonymisation of labels even under safety level 0
#80
ViralVerity
closed
3 years ago
0
pull cog to artic
#79
aineniamh
closed
3 years ago
0
feature request from user
#78
aineniamh
closed
3 years ago
0
adm2 in input csv breaks --local-lineages
#77
aineniamh
closed
3 years ago
0
report breaks colouring by trait defaults
#76
aineniamh
closed
3 years ago
0
Report breaks if phylotype not supplied
#75
aineniamh
closed
3 years ago
0
Nottinghamshire gets mapped to `SUTTON-IN-ASHFIELD` for some reason
#74
rambaut
closed
3 years ago
1
--cluster civet and --update civet
#73
aineniamh
closed
3 years ago
0
overwriting config and check args rather than arg, config default
#72
aineniamh
closed
3 years ago
0
add gene annotations onto the snipit graphs
#71
aineniamh
opened
3 years ago
1
Remove pweave from template
#70
ViralVerity
closed
3 years ago
1
Get adjacent adm2 in a better way for outer postcode/coord map
#69
ViralVerity
closed
3 years ago
0
Optimise parse metadata step
#68
ViralVerity
closed
3 years ago
0
docs update
#67
aineniamh
closed
3 years ago
0
Config dev
#66
aineniamh
closed
3 years ago
0
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