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jbloomlab
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polyclonal
Model mutational escape from polyclonal antibodies.
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fix max in distinct epitopes `altair` plots
#85
jbloom
closed
2 years ago
1
Shrink `specify_epitopes` and `partition_function` notebooks
#84
timcyu
closed
2 years ago
0
adjust regularization
#83
jbloom
closed
2 years ago
0
adjust regularization weights
#82
jbloom
closed
2 years ago
0
add real monoclonal antibody from REGN10933 deep mutational scanning
#81
jbloom
closed
2 years ago
0
add real example
#80
jbloom
closed
2 years ago
0
shrink overly large notebooks
#79
jbloom
closed
2 years ago
0
update plots and `altair`
#78
jbloom
closed
2 years ago
1
improve calculation of site summary escape
#77
jbloom
closed
2 years ago
0
remove median from bootstrap results
#76
jbloom
closed
2 years ago
0
improve site-level metrics and filtering of poorly fit mutations
#75
jbloom
closed
2 years ago
0
allow filtering by times mutation seen
#74
jbloom
closed
2 years ago
0
report number of variants with mutation
#73
jbloom
closed
2 years ago
0
Highlight mutations with high uncertainty in heat maps
#72
zorian15
closed
2 years ago
5
improve plots
#71
jbloom
closed
2 years ago
0
allow gaps
#70
jbloom
closed
2 years ago
0
60 bootstrap predictions
#69
zorian15
closed
2 years ago
1
describe bootstrapping implementation
#68
jbloom
closed
2 years ago
0
add `RBD_bootstrap` to tests and examples in docs
#67
jbloom
closed
2 years ago
0
plot site-level lineplot for bootstrapped fits
#66
jbloom
closed
2 years ago
0
plot heatmaps for bootstrap
#65
jbloom
closed
2 years ago
0
ensure bootstrap is per variant
#64
jbloom
closed
2 years ago
0
plot bootstrapped wildtype activities.
#63
jbloom
closed
2 years ago
2
bootstrapping maybe isn't quite right
#62
jbloom
closed
2 years ago
3
add `PolyclonalCollection.activity_wt_barplot`
#61
jbloom
closed
2 years ago
0
additional output functions of `PolyclonalCollection`
#60
jbloom
closed
2 years ago
1
Bootstrapping summarize
#59
jbloom
closed
2 years ago
1
seed bootstrap replicates intelligently and start example notebook
#58
jbloom
closed
2 years ago
0
harmonize epitopes by name
#57
jbloom
closed
2 years ago
1
fix plots in concentration_set
#56
timcyu
closed
2 years ago
1
bootstrapping example notebook
#55
jbloom
closed
2 years ago
0
change default `collapse_identical_variants` to `False`
#54
jbloom
closed
2 years ago
0
change default value of `collapse_identical_variants`
#53
jbloom
closed
2 years ago
0
problems with plotting in `concentration_set`
#52
jbloom
closed
2 years ago
0
docs fixes, mostly for bootstrapping
#51
jbloom
closed
2 years ago
0
Update altair to 4.2 and re-run fitting
#50
timcyu
closed
2 years ago
0
45 plotting extensions for bootstrapping
#49
zorian15
closed
2 years ago
1
bootstrapping on realistic data set
#48
jbloom
closed
2 years ago
1
make `Polyclonal` fitting and harmonization errors more specific
#47
jbloom
closed
2 years ago
0
44 interaction effects
#46
timcyu
closed
2 years ago
1
Extend plotting code to bootstrap summary statistics
#45
zorian15
closed
2 years ago
3
Explore consequences of interaction effects between mutations
#44
timcyu
closed
2 years ago
2
15 bootstrap
#43
zorian15
closed
2 years ago
14
Add epitope correlation heatmaps
#42
zorian15
closed
2 years ago
3
use `mushi.optimization` module (newly-available in python >3.7)
#41
wsdewitt
closed
1 year ago
1
Overlapping vs. Distinct epitopes
#40
timcyu
closed
2 years ago
2
38 epitope harmony
#39
zorian15
closed
2 years ago
19
Implement epitope harmonization for polyclonal objects
#38
matsen
closed
2 years ago
0
re-run notebooks and fix `Altair` plots
#37
jbloom
closed
2 years ago
3
modify site-spread regularization to pass test
#36
jbloom
closed
2 years ago
1
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