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jbloomlab
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polyclonal
Model mutational escape from polyclonal antibodies.
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add `mean_abs` and `sum_abs` to `lineplot_and_heatmap`
#183
jbloom
closed
5 months ago
0
improve stat hiding filters in `lineplot_and_heatmap`
#182
jbloom
closed
5 months ago
0
Added `rename_std` option to `lineplot_and_heatmaps`
#181
jbloom
closed
8 months ago
0
in `lineplot_and_heatmap`, apply `rename_stat_col` to `<stat>_std` column
#180
jbloom
closed
8 months ago
0
enabling filtering of plots by standard deviation of measurements
#179
jbloom
closed
8 months ago
0
Ensure that wildtype identity is always shown in heatmap tooltips even if mutation is filtered
#178
jbloom
closed
10 months ago
0
improve heatmap limits
#177
jbloom
closed
10 months ago
0
heatmap shows as grayed out filtered mutations even w no escape measured
#176
jbloom
closed
10 months ago
0
add `min_times_seen` to `PolyclonalCollection.mut_escape_corr`
#175
jbloom
closed
10 months ago
0
fix `mut_icXX` bug and increase bounds
#174
jbloom
closed
11 months ago
0
fix bug in `PolyclonalCollection.sites` when models have different sequential integer sites
#173
jbloom
closed
11 months ago
0
switch to testing via GitHub Actions rather than Travis
#172
jbloom
closed
11 months ago
0
ensure `PolyclonalCollection.sites` is always defined
#171
jbloom
closed
11 months ago
0
correct implementation of `check_wt_icXX` (becomes version 6.2)
#170
jbloom
closed
1 year ago
0
expand `icXX` methods range
#169
jbloom
closed
1 year ago
0
check_wt_icXX lower bound is too restrictive for potent sera
#168
fwelsh
closed
1 year ago
6
add `PolyclonalCollection.mut_icXX_*` methods
#167
jbloom
closed
1 year ago
0
Add `mut_icXX_plot` and `mut_icXX_df` methods to `Polyclonal`.
#166
jbloom
closed
1 year ago
0
change linting from `flake8` to `ruff`
#165
jbloom
closed
1 year ago
0
upgrade minimum `altair` to 5.0.0
#164
jbloom
closed
1 year ago
0
add "min_magnitude" `avg_type` for mut escape in `PolyclonalCollection`
#163
jbloom
closed
1 year ago
0
fold change ICXX plots
#162
jbloom
closed
1 year ago
0
using spacial distances masks some escape sites
#161
Bernadetadad
opened
1 year ago
7
use `altair` version 5.0
#160
jbloom
closed
1 year ago
0
increase default `reg_activity_weight` from 1.0 to 2.0
#159
jbloom
closed
1 year ago
0
fit model with fixed Hill coefficient and non-neutralized fraction first
#158
jbloom
closed
1 year ago
0
change Hill coefficient regularization
#157
jbloom
closed
1 year ago
0
bounds to `Polyclonal.fit` as params rather than harcoded
#156
jbloom
closed
1 year ago
0
Remove `is_weighted_replicate` from `curves_plot` tooltip
#155
jbloom
closed
1 year ago
0
Add `sites_to_show` to `polyclonal.plot.lineplot_and_heatmap` (becomes version 4.1)
#154
jbloom
closed
1 year ago
0
Add option to exclude a list of sites from escape plotting
#153
caelanradford
closed
1 year ago
1
remove `is_weighted_replicate` from `PolyclonalCollection.curves_plot` tooltip.
#152
jbloom
closed
1 year ago
0
generalize Hill curves (version 4.0)
#151
jbloom
closed
1 year ago
1
epitope colours
#150
Bernadetadad
closed
1 year ago
2
default fitting parameters?
#149
jbloom
closed
1 year ago
6
improve plotting and allow heatmaps to hide rather than filter mutations
#148
jbloom
closed
1 year ago
0
Show heatmap tooltip null numerical values as NaN
#147
jbloom
closed
1 year ago
0
visualize per-model measurements for averages of models
#146
jbloom
closed
1 year ago
0
enable user-specified fixed limits on heatmap ranges
#145
jbloom
closed
1 year ago
0
enable visualization of filtered mutations
#144
jbloom
closed
1 year ago
1
Allow cif files for PDB structures
#143
Bernadetadad
closed
1 year ago
1
customization options for escape plotting
#142
jbloom
closed
1 year ago
1
Option for line plot or heatmap only in `model.mut_escape_plot()`
#141
fwelsh
closed
1 year ago
0
Allow str site numbers in `reassign_b_factor` (v 3.2)
#140
jbloom
closed
1 year ago
0
Allow non-int site numbers in PDB b-factor reassignment
#139
fwelsh
closed
1 year ago
2
Change default positive colors
#138
timcyu
closed
1 year ago
3
Epitope colors for polyclonal
#137
timcyu
closed
1 year ago
6
version 3.0: adjust regularization weights, add examples
#136
jbloom
closed
1 year ago
2
implementation of uniqueness regularization
#135
jbloom
closed
1 year ago
0
implement spatial regularization
#134
jbloom
closed
1 year ago
0
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