dms-vep SARS-CoV-2_XBB.1.5_spike_DMS issues

dms-vep / SARS-CoV-2_XBB.1.5_spike_DMS

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compare growth rates from Murrell and Bedford

#84 jbloom closed 5 months ago
0
add `compare_natural` for BA.2 + BA.5 + XBB clades

#83 jbloom closed 5 months ago
0
Mutation fitness correlations by spike domain

#82 Bernadetadad opened 5 months ago
2
Assign distance to ACE2 to binding correlations

#81 jbloom closed 5 months ago
0
create `escape_by_prior_infections` notebook in docs

#80 jbloom closed 5 months ago
0
Assign distance to ACE2 to binding correlations

#79 Bernadetadad closed 5 months ago
1
Group serum escape by number of previous infections

#78 Bernadetadad closed 5 months ago
2
comparison of predictions to BA.2.86 evolution

#77 jbloom closed 5 months ago
0
update to March-1-2024 Pango definitions and look at coverage of BA.2.86 clade mutations

#76 jbloom closed 6 months ago
0
XBB.1.5 ACE2 binding correlation to BA.2 and yeast DMS

#75 Bernadetadad closed 5 months ago
4
Add BA.2.86 to natural sequence comparison

#74 Bernadetadad closed 6 months ago
1
Include BA.2.86 in table showing how many mutations our library covers

#73 Bernadetadad closed 6 months ago
0
`compare_natural` now shows trees w clade growth / growth changes, and hist for OLS P-value randomizations

#72 jbloom closed 10 months ago
0
added `muts_per_clade` notebook plotting mutations per clade

#71 jbloom closed 10 months ago
0
improve comparison to natural sequences

#70 jbloom closed 10 months ago
0
format svg files

#69 Bernadetadad closed 10 months ago
0
binding versus escape correlation for sites with lots of escape, integrated into pipeline

#68 jbloom closed 10 months ago
0
Plot binding vs escape

#67 Bernadetadad closed 10 months ago
1
plot key sites in logo plots: sites w lots of escape, and sites used in neuts

#66 jbloom closed 10 months ago
0
adjust ACE2 slider default to -2 in summaries

#65 jbloom closed 10 months ago
0
rename ACE2 affinity to ACE2 binding throughout repo

#64 jbloom closed 10 months ago
0
is ACE2 filter too stringent in `summaries_config.yml`

#63 jbloom closed 10 months ago
1
filter noisy measurements

#62 jbloom closed 10 months ago
0
Change from ACE2 affinity to spike ACE2 binding

#61 Bernadetadad closed 10 months ago
2
make logo plots for key sera escape mutations

#60 jbloom closed 10 months ago
1
filter mutations with very large differences between libraries? (eg, K304Q)

#59 jbloom closed 10 months ago
1
use randomization to compute P-values and distributions of growth changes among clades

#58 jbloom closed 10 months ago
0
`compare_natural` includes clade pairs with multiple spike mutations and also plots phenotypes of clades

#57 jbloom closed 10 months 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 10 months ago
0
ACE2 vs affinity correlations for specific sites

#55 Bernadetadad closed 10 months ago
12
Clade growth newer data

#54 jbloom closed 10 months ago
0
plot effects of key mutations on cell entry

#53 jbloom closed 10 months ago
0
clamp affinity_dist plot

#52 jbloom closed 10 months ago
0
clamp range of affinities in RBD / non-RBD ACE2 affinity effects

#51 jbloom closed 10 months ago
1
make a distribution plot of cell entry effects showing key mutations

#50 jbloom closed 10 months ago
1
add non-RBD ACE2 affinity enhancing mutations in BA.2 / BA.5 pango clades

#49 jbloom closed 11 months ago
0
correlate functional effects w natural sequence fitness estimates and between strains

#48 jbloom closed 11 months ago
0
Functional correlations

#47 Bernadetadad closed 10 months ago
3
box plots of distributions of mutation effects

#46 jbloom closed 11 months ago
0
figure of mutation effects on cell entry by domain and mutation type

#45 jbloom closed 11 months ago
5
change functional filter

#44 Bernadetadad closed 11 months ago
0
tabulate non-RBD mutations increasing ACE2 affinity in recent clades and coverage of clade mutations

#43 jbloom closed 11 months ago
0
change clippings

#42 Bernadetadad closed 11 months ago
0
RBD expression filter

#41 Bernadetadad closed 11 months ago
1
effect of filters on escape

#40 jbloom closed 11 months ago
1
color correlations RBD / non RBD

#39 Bernadetadad closed 11 months ago
2
Set func effects

#38 Bernadetadad closed 11 months ago
0
Heatmap scale

#37 Bernadetadad closed 11 months ago
0
Revert "Adjust summary heatmap scale"

#36 Bernadetadad closed 11 months ago
0
Adjust summary heatmap scale

#35 Bernadetadad closed 11 months ago
0