Giters
mcveanlab
/
treeseq-inference
Work for the tree sequence inference paper.
Geek Repo:
Geek Repo
Github PK Tool:
Github PK Tool
Stargazers:
23
Watchers:
7
Issues:
59
Forks:
9
mcveanlab/treeseq-inference Issues
Add requirement for R "ape" library >= 4.0-0.2
Closed
3 months ago
Comments count
2
Yet another argweaver bug
Closed
3 months ago
Version of bgen library required to build the simplebgen module
Updated
a year ago
Comments count
1
How do I create "data/1kg_gnn.csv"?
Updated
2 years ago
Comments count
4
Availability of UKB tree sequences and GNN
Closed
2 years ago
Comments count
3
Error in msprime Out-of-Africa model
Updated
4 years ago
Change selective sweep code to use SLiM
Closed
6 years ago
Comments count
4
Making empirical error faster
Closed
6 years ago
Comments count
9
Add documentation for running evaluations
Closed
6 years ago
Comments count
1
Add code to generate 1kg_chr_20_sample_edges figure.
Closed
6 years ago
Comments count
2
Add code to produce figure S1.
Closed
6 years ago
Comments count
2
Cleanup required
Closed
6 years ago
Comments count
7
Add plots for SGDP regions
Closed
6 years ago
Central plotting script
Closed
6 years ago
Issue cleanup
Closed
6 years ago
Comments count
1
Polytomy resolution observations
Closed
6 years ago
Comments count
1
Statistics for measuring how we do with real data
Updated
6 years ago
Comments count
4
Ideas for checking on accuracy of ARG reconstruction
Closed
6 years ago
Comments count
1
Calculate likelihood of observed pattern of variants, given a tree sequence
Closed
6 years ago
Comments count
1
adding unphased (e.g. ancient) DNA
Closed
6 years ago
Comments count
1
Adjust compression metrics to account for polytomies
Closed
6 years ago
Comments count
1
Save some measures of size & number of polytomies
Closed
6 years ago
Comments count
1
discretise_mutations() in msprime_extras no longer works
Closed
6 years ago
Comments count
1
Cannot run metric calculation at same time as processing
Closed
6 years ago
Comments count
6
Future projects
Closed
6 years ago
Comments count
1
How do stats deal with polytomies (created by ts-infer)
Closed
6 years ago
Comments count
3
Argweaver must be installed to work?
Closed
6 years ago
Comments count
1
RENTplus error
Closed
6 years ago
Comments count
2
Test with gene conversion
Updated
6 years ago
Parallel setup doesn't work
Closed
6 years ago
Comments count
4
ARGmetrics returns NaN for non binary trees
Closed
8 years ago
Comments count
3
Too much stuff in Git
Closed
8 years ago
Comments count
2
Combine infer and process steps
Closed
8 years ago
Comments count
2
Error in tsinf for single locus
Closed
8 years ago
Minor - set "quiet" output for ARGweaver
Closed
8 years ago
Comments count
2
Strange ARGweaver behaviour at large mutation rates
Closed
8 years ago
Comments count
20
Add Kendall-Colijn stat to tree metrics
Closed
8 years ago
Comments count
2
tsinfer bug from latest msprime
Closed
8 years ago
Comments count
5
Killing plots.py does not kill inference subprocesses
Closed
8 years ago
Comments count
9
Metrics complain of "one tree is unrooted, unrooted both"
Closed
8 years ago
Comments count
1
Check if smc2arg bug is simply relabelling tips
Closed
8 years ago
Comments count
4
Assess adequacy of burn-in period for ARGweaver inference
Updated
8 years ago
Comments count
2
ARGweaver inference step does not properly record mem/cpu
Closed
8 years ago
Comments count
2
Another argweaver bug
Closed
8 years ago
Comments count
5
Cannot discretise X mutations in interval
Closed
8 years ago
Comments count
1
Argweaver working?
Closed
8 years ago
Comments count
3
Update tsinf to include site positions
Closed
8 years ago
Comments count
1
Save variant positions in .npy file
Closed
8 years ago
Comments count
6
Variant positions need to be unique integers
Closed
8 years ago
Comments count
1
Can't export newick trees - is `simplify` working OK?
Closed
8 years ago
Comments count
16
Previous
Next