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what-is-an-arg-paper
Manuscript and code for the "What is an ARG?" paper
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Use correct recombination rate in Drosophila inference
#420
hyanwong
closed
9 months ago
0
Rewrite abstract
#419
jeromekelleher
closed
10 months ago
0
Fixup eARG refs
#418
jeromekelleher
closed
10 months ago
0
Various clarifications and cleanups
#417
jeromekelleher
closed
10 months ago
0
Substantial rejig of s9
#416
jeromekelleher
closed
10 months ago
0
Move Wiuf & Hein caveat
#415
hyanwong
closed
10 months ago
3
Add data availability section
#414
hyanwong
closed
10 months ago
1
Edits for s5 through s7
#413
jeromekelleher
closed
10 months ago
0
Pass through sections 1 through 3
#412
jeromekelleher
closed
10 months ago
0
Mention that eARG recombination nodes are (by definition) unary
#411
hyanwong
closed
10 months ago
1
Darken background that highlights genetic regions in the ts
#410
hyanwong
closed
10 months ago
0
Pass through intro
#409
jeromekelleher
closed
10 months ago
0
Pass through discussion and light edits to appendix
#408
jeromekelleher
closed
10 months ago
0
Latter sections pass
#407
jeromekelleher
closed
10 months ago
0
Restructure "local trees" section
#406
jeromekelleher
closed
10 months ago
2
More gregor comments
#405
jeromekelleher
closed
10 months ago
0
Some edits from Gregor
#404
jeromekelleher
closed
10 months ago
0
Remove SI units
#403
jeromekelleher
closed
10 months ago
1
Clarify or remove Relate description
#402
hyanwong
closed
10 months ago
2
Place tool config in a single file
#401
hyanwong
closed
10 months ago
0
Placement of the ref to Lewanski
#400
hyanwong
closed
10 months ago
2
Add (json?) file specifying inference params etc.
#399
hyanwong
closed
10 months ago
1
Inference para
#398
hyanwong
closed
10 months ago
5
added Genome position (kb) axis label
#397
awohns
closed
10 months ago
4
Bug fix: need to check which edge is left and which is right
#396
a-ignatieva
closed
10 months ago
0
Content reshuffle
#395
jeromekelleher
closed
10 months ago
0
Add SCAR paper
#394
jeromekelleher
closed
10 months ago
0
New section to describe example ARGs
#393
jeromekelleher
closed
10 months ago
6
Cite https://doi.org/10.1371/journal.pcbi.1010422
#392
jeromekelleher
closed
10 months ago
3
Add Fan et al 2023
#391
jeromekelleher
closed
10 months ago
0
Tsinfer figure is without "root breaking"
#390
hyanwong
closed
10 months ago
3
Reference Fan et al preprint
#389
jeromekelleher
closed
10 months ago
1
Add details on inference methods for fig
#388
jeromekelleher
closed
10 months ago
2
Fix supplement
#387
jeromekelleher
closed
10 months ago
0
Explain bottom row of inferred ARGs fig
#386
jeromekelleher
closed
10 months ago
1
Remove notebooks dir
#385
hyanwong
closed
10 months ago
0
Make symbols round in fig 1
#384
hyanwong
closed
10 months ago
0
Edit pass 2
#383
jeromekelleher
closed
10 months ago
0
Cite GeL paper
#382
gregorgorjanc
closed
10 months ago
5
Adding tables for gARG #348 and other bits
#381
gregorgorjanc
closed
10 months ago
1
Converting eARG to gARG - reprise
#380
hyanwong
closed
10 months ago
0
Change labelling from N trees to N-1 breakpoints
#379
hyanwong
closed
10 months ago
0
Second pass at prospective/retrospective
#378
hyanwong
closed
10 months ago
0
Make recombination lines thicker
#377
hyanwong
closed
10 months ago
0
Make the inference plots a bit less tall
#376
hyanwong
closed
10 months ago
2
Add the actual plots
#375
hyanwong
closed
10 months ago
0
Tweaks to gARG section
#374
jeromekelleher
closed
10 months ago
0
Make samples square nodes
#373
hyanwong
closed
10 months ago
0
Add text about cell lineages
#372
hyanwong
closed
10 months ago
0
Update cites
#371
jeromekelleher
closed
10 months ago
0
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