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jeromekelleher
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sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Only plot if no axis defined
#142
hyanwong
closed
1 year ago
0
Add fwd_bck_parents_max_mut_dist to breakpoint table
#141
hyanwong
closed
1 year ago
4
Always add number of descendant samples
#140
hyanwong
closed
1 year ago
3
Removing unary nodes in viz
#139
a-ignatieva
closed
1 year ago
0
Fixing missing GISAID lineages
#138
a-ignatieva
closed
1 year ago
0
TreeInfo can use alternative Pango classifications
#137
hyanwong
closed
1 year ago
5
Sample subgraph labels and colours
#136
hyanwong
closed
1 year ago
2
Allow axis passing to sample_subgraph
#135
hyanwong
closed
1 year ago
0
Turn "lineage_imputation" into a script
#134
hyanwong
opened
1 year ago
2
Sample QC metadata
#133
szhan
opened
1 year ago
2
"Redundant" unary nodes
#132
hyanwong
opened
1 year ago
6
Improving subgraph plots
#131
a-ignatieva
closed
1 year ago
0
Pango lineage XAG groups with a few XAB samples
#130
hyanwong
closed
1 year ago
10
Different sources of Pango lineage status
#129
szhan
opened
1 year ago
1
is_arg_hmm_path_length_consistent too stringent?
#128
hyanwong
opened
1 year ago
0
Nextstrain-subset ARG contains recombination which majorly affects delta time origin
#127
hyanwong
opened
1 year ago
7
Get breakpoint MRCAs systematically and update single-break recombinant export
#126
jeromekelleher
closed
1 year ago
4
Check that forward HMM matches edges in ARG on export
#125
jeromekelleher
closed
1 year ago
1
Check for imputed pango lineage consistency in forward/backward parents
#124
jeromekelleher
closed
1 year ago
0
Classify non tree hmms
#123
hyanwong
closed
1 year ago
4
Correct wrong variables
#122
hyanwong
closed
1 year ago
0
Weirdness in reporting some recombination nodes
#121
hyanwong
opened
1 year ago
3
Add comment about alternative method
#120
hyanwong
closed
1 year ago
1
Add base time to top-level metadata
#119
jeromekelleher
opened
1 year ago
0
add export_recombination_node_breakpoints
#118
hyanwong
closed
1 year ago
2
Change list to dict
#117
hyanwong
closed
1 year ago
0
Add extra MRCA information to export_recombinants
#116
hyanwong
closed
1 year ago
0
"Recombinant" or "Recombination node"
#115
hyanwong
closed
1 year ago
8
Gitignore
#114
hyanwong
closed
1 year ago
0
Assertion error when calling export_recombinants
#113
szhan
closed
1 year ago
2
Allow other args (e.g. span) when making nextstrain trees
#112
hyanwong
closed
1 year ago
0
pango_recombinant_lineages_report is misleading
#111
jeromekelleher
opened
1 year ago
0
Add function to systematise exporting recombinants
#110
jeromekelleher
closed
1 year ago
1
README
#109
szhan
closed
1 year ago
0
Recombinant tables
#108
szhan
closed
1 year ago
4
Fix off by one error
#107
jeromekelleher
closed
1 year ago
0
Off-by-one error in node report for descendants
#106
jeromekelleher
closed
1 year ago
0
Add mutation spectrum plot
#105
jeromekelleher
closed
1 year ago
0
Replacement terminology for "ARG v1" (big) vs "ARG v2" (small)
#104
hyanwong
closed
1 year ago
6
Replacement terminology for "is_consistent"
#103
hyanwong
closed
1 year ago
7
Root node does not have the earliest sampling date
#102
szhan
opened
1 year ago
1
Add same-parent parsimony step for recombinants
#101
jeromekelleher
opened
1 year ago
12
Classification for non-biological reversions
#100
jeromekelleher
opened
1 year ago
13
Update RecombinantAncestry.ipynb
#99
hyanwong
opened
1 year ago
2
Add site_summary data frame
#98
jeromekelleher
opened
1 year ago
1
Add date_summary data frame
#97
jeromekelleher
opened
1 year ago
1
Fix #91
#96
hyanwong
closed
1 year ago
0
Classifying recombination nodes
#95
hyanwong
opened
1 year ago
10
Classifying reversion mutations
#94
hyanwong
opened
1 year ago
1
Add parameter search for recombinants
#93
jeromekelleher
opened
1 year ago
0
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