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dms-vep
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SARS-CoV-2_XBB.1.5_spike_DMS
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A question about data
#85
AllanLZhang
closed
1 month ago
3
compare growth rates from Murrell and Bedford
#84
jbloom
closed
9 months ago
0
add `compare_natural` for BA.2 + BA.5 + XBB clades
#83
jbloom
closed
9 months ago
0
Mutation fitness correlations by spike domain
#82
Bernadetadad
opened
9 months ago
2
Assign distance to ACE2 to binding correlations
#81
jbloom
closed
9 months ago
0
create `escape_by_prior_infections` notebook in docs
#80
jbloom
closed
9 months ago
0
Assign distance to ACE2 to binding correlations
#79
Bernadetadad
closed
9 months ago
1
Group serum escape by number of previous infections
#78
Bernadetadad
closed
9 months ago
2
comparison of predictions to BA.2.86 evolution
#77
jbloom
closed
9 months ago
0
update to March-1-2024 Pango definitions and look at coverage of BA.2.86 clade mutations
#76
jbloom
closed
9 months ago
0
XBB.1.5 ACE2 binding correlation to BA.2 and yeast DMS
#75
Bernadetadad
closed
9 months ago
4
Add BA.2.86 to natural sequence comparison
#74
Bernadetadad
closed
9 months ago
1
Include BA.2.86 in table showing how many mutations our library covers
#73
Bernadetadad
closed
9 months ago
0
`compare_natural` now shows trees w clade growth / growth changes, and hist for OLS P-value randomizations
#72
jbloom
closed
1 year ago
0
added `muts_per_clade` notebook plotting mutations per clade
#71
jbloom
closed
1 year ago
0
improve comparison to natural sequences
#70
jbloom
closed
1 year ago
0
format svg files
#69
Bernadetadad
closed
1 year ago
0
binding versus escape correlation for sites with lots of escape, integrated into pipeline
#68
jbloom
closed
1 year ago
0
Plot binding vs escape
#67
Bernadetadad
closed
1 year ago
1
plot key sites in logo plots: sites w lots of escape, and sites used in neuts
#66
jbloom
closed
1 year ago
0
adjust ACE2 slider default to -2 in summaries
#65
jbloom
closed
1 year ago
0
rename ACE2 affinity to ACE2 binding throughout repo
#64
jbloom
closed
1 year ago
0
is ACE2 filter too stringent in `summaries_config.yml`
#63
jbloom
closed
1 year ago
1
filter noisy measurements
#62
jbloom
closed
1 year ago
0
Change from ACE2 affinity to spike ACE2 binding
#61
Bernadetadad
closed
1 year ago
2
make logo plots for key sera escape mutations
#60
jbloom
closed
1 year ago
1
filter mutations with very large differences between libraries? (eg, K304Q)
#59
jbloom
closed
1 year ago
1
use randomization to compute P-values and distributions of growth changes among clades
#58
jbloom
closed
1 year ago
0
`compare_natural` includes clade pairs with multiple spike mutations and also plots phenotypes of clades
#57
jbloom
closed
1 year ago
0
update natural comparison to look at clade pairs differing by one spike mutation and change in DMS vs change in growth
#56
jbloom
closed
1 year ago
0
ACE2 vs affinity correlations for specific sites
#55
Bernadetadad
closed
1 year ago
12
Clade growth newer data
#54
jbloom
closed
1 year ago
0
plot effects of key mutations on cell entry
#53
jbloom
closed
1 year ago
0
clamp affinity_dist plot
#52
jbloom
closed
1 year ago
0
clamp range of affinities in RBD / non-RBD ACE2 affinity effects
#51
jbloom
closed
1 year ago
1
make a distribution plot of cell entry effects showing key mutations
#50
jbloom
closed
1 year ago
1
add non-RBD ACE2 affinity enhancing mutations in BA.2 / BA.5 pango clades
#49
jbloom
closed
1 year ago
0
correlate functional effects w natural sequence fitness estimates and between strains
#48
jbloom
closed
1 year ago
0
Functional correlations
#47
Bernadetadad
closed
1 year ago
3
box plots of distributions of mutation effects
#46
jbloom
closed
1 year ago
0
figure of mutation effects on cell entry by domain and mutation type
#45
jbloom
closed
1 year ago
5
change functional filter
#44
Bernadetadad
closed
1 year ago
0
tabulate non-RBD mutations increasing ACE2 affinity in recent clades and coverage of clade mutations
#43
jbloom
closed
1 year ago
0
change clippings
#42
Bernadetadad
closed
1 year ago
0
RBD expression filter
#41
Bernadetadad
closed
1 year ago
1
effect of filters on escape
#40
jbloom
closed
1 year ago
1
color correlations RBD / non RBD
#39
Bernadetadad
closed
1 year ago
2
Set func effects
#38
Bernadetadad
closed
1 year ago
0
Heatmap scale
#37
Bernadetadad
closed
1 year ago
0
Revert "Adjust summary heatmap scale"
#36
Bernadetadad
closed
1 year ago
0
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