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jbloomlab
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polyclonal
Model mutational escape from polyclonal antibodies.
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flatten escape values at near-zero sites in RBD simulated data
#133
jbloom
closed
1 year ago
0
Epitopes are questionably separated despite the epitope similarity penalty
#132
caelanradford
closed
1 year ago
4
fix assert statement in reg_similarity
#131
timcyu
closed
1 year ago
0
implement epitope similarity regularization with absolute value approximation
#130
timcyu
closed
1 year ago
7
fix bug in wildtype heatmap plot introduced in 2.3
#129
jbloom
closed
1 year ago
0
implement epitope similarity regularization
#128
timcyu
closed
1 year ago
8
`lineplot_and_heatmap` compute heatmap range after applying min specified for sliders
#127
jbloom
closed
1 year ago
0
allow `data_mut_escape_overlap` != "exact" even with `sites` set
#126
jbloom
closed
1 year ago
1
add reference to Yu et al citation
#125
jbloom
closed
1 year ago
0
A regularization term that penalizes similarity between epitope escape profiles
#124
timcyu
closed
1 year ago
28
Reference sites cannot be used when initializing a polyclonal model with site or mutation escape dataframes
#123
caelanradford
closed
1 year ago
0
Add preprint link to docs
#122
timcyu
closed
1 year ago
1
add citations to pre-print
#121
jbloom
closed
1 year ago
0
Windows specific int comparison error
#120
Caleb-Carr
opened
1 year ago
1
Update experimental design notebooks
#119
timcyu
closed
1 year ago
0
fixes / improvements to mut escape plotting
#118
jbloom
closed
1 year ago
0
change escape plots (version 2.0)
#117
jbloom
closed
1 year ago
0
allow negative site numbers
#116
jbloom
closed
1 year ago
0
`PolyclonalCollection` still works if just one model
#115
jbloom
closed
1 year ago
0
fixing two silly typos
#114
matsen
closed
1 year ago
0
keep sites correctly sorted in `PolyclonalCollection` output
#113
jbloom
closed
1 year ago
0
heatmaps never filter wildtype with slider stats
#112
jbloom
closed
1 year ago
0
biochemically order amino-acids for heatmap plotting
#111
jbloom
closed
1 year ago
0
enable non-sequential-integer reference site numbering
#110
jbloom
closed
1 year ago
0
order amino-acid alphabets differently?
#109
jbloom
closed
1 year ago
1
select mutation escape values by number of models in which they are seen
#108
jbloom
closed
1 year ago
0
Fix `SettingWithCopyWarning` in heatmap plotting
#107
jbloom
closed
1 year ago
0
enable calculation of median as average in `PolyclonalCollection`, make default for `PolyclonalAverage`
#106
jbloom
closed
1 year ago
0
fix `pandas` warning from `polyclonal.plot` heatmap
#105
jbloom
closed
1 year ago
0
docs give installation instructions for 1.0
#104
jbloom
closed
1 year ago
1
reference site numbering
#103
jbloom
closed
1 year ago
1
filter by number of models in `PolyclonalCollection` plots
#102
jbloom
closed
1 year ago
0
plot / compute average as median in addition to mean
#101
jbloom
closed
1 year ago
0
notebooks test and plot `PolyclonalAverage`
#100
jbloom
closed
1 year ago
0
plot mut escape correlation heatmaps
#99
jbloom
closed
1 year ago
0
implement `PolyclonalAverage`
#98
jbloom
closed
1 year ago
0
`harmonize_epitopes_with` -> `epitope_harmonized_model` and add `tidy_to_corr`
#97
jbloom
closed
1 year ago
0
generalize `PolyclonalCollection` and implement `PolyclonalBootstrap`
#96
jbloom
closed
1 year ago
0
average across `Polyclonal` models
#95
jbloom
closed
1 year ago
0
Re-run fitting in some notebooks and make epitope colors consistent in figures
#94
timcyu
closed
2 years ago
0
Further generalize `mut_escape_heatmap`
#93
jbloom
closed
2 years ago
0
generalize `mut_escape_heatmap`
#92
jbloom
closed
2 years ago
0
add installation instructions from GitHub
#91
jbloom
closed
2 years ago
0
license that is free for non-profit/academic use but request licensing for profit
#90
jbloom
closed
2 years ago
0
regularize epitope activities
#89
jbloom
closed
2 years ago
0
fix bug in parameter check in `Polyclonal`
#88
jbloom
closed
2 years ago
0
ensure epitope names are str, not int
#87
jbloom
closed
2 years ago
0
Fixes barplot scale to [0,1]
#86
timcyu
closed
2 years ago
0
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
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