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nextstrain
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fauna
RethinkDB database to support real-time virus analysis
GNU Affero General Public License v3.0
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Use custom runtime
#170
victorlin
opened
4 days ago
2
Support pandas version 2
#169
victorlin
closed
3 days ago
5
Pylint alerts corrections as part of an intervention experiment
#168
evidencebp
closed
4 days ago
1
vidrl_upload: Update `VACCINE_MAPPING` to match proxies
#167
joverlee521
closed
2 weeks ago
1
vidrl_upload: fix `serum_strain` used for human sera measurements
#166
joverlee521
closed
2 weeks ago
2
seasonal flu "virus" records should be indexed by isolate id instead of strain name
#165
huddlej
opened
1 month ago
0
Update ingest for VIDRL flat files
#164
joverlee521
opened
1 month ago
0
Generate list of new titers references on each new ingest
#163
huddlej
opened
2 months ago
1
Decouple data curation and upload
#162
joverlee521
opened
2 months ago
0
Revisit ingestion of VIDRL flat files
#161
joverlee521
opened
2 months ago
7
Ingest VIDRL human sera references
#160
joverlee521
closed
2 months ago
3
crick_upload: Skip "comments" sheets
#159
joverlee521
closed
3 months ago
1
Parse VIDRL human sera pool measurements
#158
huddlej
opened
3 months ago
2
Refactor `vidrl_upload` to auto-detect titer info
#157
j23414
closed
4 months ago
0
Publish to pypi and then bioconda
#156
corneliusroemer
opened
4 months ago
1
Update readme
#155
tsibley
closed
4 months ago
0
adding syntax to check for cattle sequences and add cattle as a disti…
#154
lmoncla
closed
7 months ago
0
vdb/flu_upload: parse `submitting_lab` from XLS
#153
joverlee521
closed
7 months ago
4
Update zika instructions
#152
j23414
closed
10 months ago
0
script/delete_records: Add option to match fields with regex pattern
#151
joverlee521
opened
1 year ago
2
requirements: Skip rethinkdb v2.4.10
#150
joverlee521
closed
1 year ago
2
Fix GISAID avian flu accessions
#149
joverlee521
closed
12 months ago
1
Fix GISAID flu accessions
#148
joverlee521
closed
1 year ago
1
Update zika instructions
#147
j23414
closed
12 months ago
2
tdb/elife_upload: Update assay_date parsing
#146
joverlee521
opened
1 year ago
0
TLS support
#145
tsibley
closed
1 year ago
0
Revisit tdb/upload's `index_fields`
#144
joverlee521
opened
1 year ago
1
Delete records with date intervals
#143
joverlee521
closed
1 year ago
0
Support ingest of individual-level human serology data for seasonal flu viruses
#142
huddlej
opened
1 year ago
0
Automate backup of Fauna databases to S3
#141
joverlee521
closed
1 year ago
4
Gisaid clade and download changes
#140
lmoncla
closed
1 year ago
0
Replace nextstrain remote with aws commands
#139
j23414
closed
4 months ago
1
tdb/download: correct flu type in strain names
#138
joverlee521
closed
1 year ago
1
Avian flu upload additions
#136
lmoncla
closed
1 year ago
0
Geolocation assignments fail for duplicate location names
#135
joverlee521
opened
1 year ago
2
Bump express from 4.16.4 to 4.17.3
#134
dependabot[bot]
opened
1 year ago
0
Bump certifi from 2020.6.20 to 2022.12.7
#133
dependabot[bot]
opened
1 year ago
0
Bump qs and express
#132
dependabot[bot]
opened
1 year ago
0
Fix cdc uploads
#131
joverlee521
closed
1 year ago
2
Assign correct host to titers from non-ferret hosts (e.g., human and mouse)
#130
huddlej
closed
1 year ago
0
serum_passage_category should be set to "egg" instead of "cell" for CDC human pool data like "L21/22 H3-EGG HUMAN POOL"
#129
huddlej
closed
1 year ago
7
feat: BV-BRC support
#128
j23414
closed
4 months ago
2
docs: zstd
#127
j23414
closed
2 years ago
0
Set `serum_id` to `lot_number` for CDC titer imports
#126
huddlej
closed
1 year ago
4
PhantomJS not found on PATH - installation via npm install
#125
limh25
closed
2 years ago
2
Bump moment from 2.22.2 to 2.29.4
#124
dependabot[bot]
opened
2 years ago
0
Bump numpy from 1.19.4 to 1.22.0
#123
dependabot[bot]
opened
2 years ago
0
docs: update dengue instructions
#122
j23414
closed
2 years ago
0
fauna downloads fail with Python 3.10
#121
huddlej
closed
1 week ago
1
preprocess sed command
#120
j23414
closed
2 years ago
0
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