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jeromekelleher
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sc2ts-paper
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Add ability to exclude positions (on by default) in lineage imputation
#247
hyanwong
closed
19 hours ago
0
Fully worked out usher conversion
#246
jeromekelleher
closed
5 days ago
0
Output details of missing lineage mutations in lineage imputation
#245
hyanwong
opened
1 week ago
1
Nucleotide mutations for Usher tree
#244
jeromekelleher
opened
1 week ago
2
Imputation update
#243
a-ignatieva
closed
1 week ago
0
WIP
#242
jeromekelleher
closed
1 week ago
1
Add converter for Viridian Usher tree to tskit
#241
jeromekelleher
closed
1 week ago
3
Set imputation positions to ints
#240
hyanwong
closed
1 week ago
0
Weird bug(?) in lineage imputation
#239
hyanwong
closed
1 week ago
0
Add in functions removed from the sc2ts repo
#238
hyanwong
closed
2 weeks ago
0
Move read_in_mutations etc to this repo?
#237
jeromekelleher
closed
2 weeks ago
5
Add notebook for testing Pango lineage origin nodes
#236
hyanwong
closed
2 weeks ago
0
Remove the --internal-only flag from lineage imputation
#235
hyanwong
closed
2 weeks ago
0
Remove masked sites from lineage imputation requirements
#234
hyanwong
opened
2 weeks ago
1
Updating lineage imputation
#233
a-ignatieva
closed
2 weeks ago
0
Create run_lineage_imputation.py
#232
hyanwong
closed
2 weeks ago
0
Manual addition of select VoC samples to seed sample matching
#231
szhan
opened
2 weeks ago
0
Add max-recurrent option, tweak params
#228
jeromekelleher
closed
1 month ago
0
Initial run specification
#227
jeromekelleher
closed
1 month ago
0
Origins of delta, for comparison
#226
hyanwong
opened
1 month ago
7
Origins of Alpha
#225
hyanwong
opened
1 month ago
7
Site filtering
#224
jeromekelleher
closed
1 month ago
0
Add Nextstrain clade labels to node metadata
#223
szhan
opened
2 months ago
2
Visualisation of simplified backbone phylogenies
#222
szhan
opened
2 months ago
4
Comparing mutation sets above Pango lineage roots
#221
szhan
opened
2 months ago
0
Paragraph on trade-offs between removing time travellers and capturing early stages of an outbreak
#220
hyanwong
opened
2 months ago
0
QC based on branch length
#217
jeromekelleher
closed
2 months ago
1
Variant-specific mutational spectra
#216
szhan
opened
2 months ago
1
Nodes with larger polytomies in the Viridian ARG
#215
hyanwong
opened
2 months ago
13
List recombination nodes by likelihood ratio of recombinants vs no recombination
#214
hyanwong
opened
2 months ago
0
Identify recombinants which we are reasonably certain of, which have not previously been detected
#213
hyanwong
opened
2 months ago
2
Add script to run MAFFT plus test files
#212
szhan
closed
2 months ago
0
Add script to run MAFFT on cluster
#211
szhan
closed
2 months ago
0
Notes on preprocessing data for run on Viridian 0.4
#210
szhan
opened
2 months ago
1
Deduplicate samples and trim columns in metadata
#209
szhan
closed
2 months ago
0
Add Makefile commands to generate csv datafiles such as `data/long_arg_recombinants.csv`
#208
hyanwong
opened
2 months ago
4
New PANGO recombinants
#207
hyanwong
opened
2 months ago
4
Do not include samples with duplicate genbank IDs
#206
hyanwong
closed
2 months ago
2
New cophylogeny
#205
hyanwong
opened
2 months ago
0
Systematise code
#204
jeromekelleher
closed
2 months ago
0
Overview of sampling dates of the entire Viridian dataset
#229
szhan
closed
1 month ago
10
Cite pyfaidx
#203
jeromekelleher
opened
3 months ago
0
Correct funding source for Ben Jeffery
#202
jeromekelleher
opened
1 year ago
0
Update README.md - add virological link
#201
hyanwong
closed
1 year ago
0
Update README.md
#200
hyanwong
closed
1 year ago
0
Investigating false positives
#199
hyanwong
opened
1 year ago
0
Fill out the README file in this repo
#198
hyanwong
closed
1 year ago
2
Document trivial filename change for wide and long ARGs
#197
hyanwong
closed
1 year ago
0
Put tanglegram-creating code into notebook
#196
hyanwong
closed
1 year ago
1
Cite recombinhunt preprint
#195
jeromekelleher
opened
1 year ago
0
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