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dms-vep
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dms-vep-pipeline
Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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Periodic Wildcard Error
#171
Bernadetadad
closed
8 months ago
1
add `show_antibody_escape_icXX_plots` option to `config.yaml`
#170
jbloom
closed
11 months ago
0
Remove 'icXX' plotting from pipeline v2
#169
fwelsh
closed
11 months ago
0
Averaging models from biological replicates actually just takes either libA or libB score
#168
fwelsh
closed
11 months ago
3
Store IC50s outside pickle file
#167
Bernadetadad
closed
11 months ago
2
upgrade to `polyclonal` 6.2
#166
jbloom
closed
1 year ago
0
show plots correctly with newer `plotnine` (becomes version 2.6.3)
#165
jbloom
closed
1 year ago
0
None of the plotnine figures are showing up
#164
bblarsen-sci
closed
1 year ago
1
upgrade `polyclonal` to 6.1
#163
jbloom
closed
1 year ago
0
fix bug in `avg_muteffects` when site numbers are str
#162
jbloom
closed
1 year ago
0
issue with avg_muteffects
#161
bblarsen-sci
closed
1 year ago
3
add mutation ICXX plots as another form of escape
#160
jbloom
closed
1 year ago
3
switch from Travis to GitHub Actions testing
#159
jbloom
closed
1 year ago
0
add ICXX values induced by mutations as a measure of escape
#158
jbloom
closed
1 year ago
0
upgrade software versions in environment (becomes version 2.5.1)
#157
jbloom
closed
1 year ago
0
Add avg_prob_escape plots from each replicate to avg_antibody_escape notebooks
#156
fwelsh
closed
11 months ago
1
When avg_type is added addtl_slider_stats reset to defaults
#155
Bernadetadad
closed
1 year ago
1
enable `min_magnitude` as plotted escape value
#154
jbloom
closed
1 year ago
0
Option to display by the smaller escape value
#153
Bernadetadad
closed
1 year ago
6
upgrade to `polyclonal` 5.2 (becomes `dms-vep-pipeline` 2.4.2)
#152
jbloom
closed
1 year ago
0
Give option to inspect antibody selection scores by concentration rather than solely averaged across replicates
#151
bblarsen-sci
closed
1 year ago
2
Sites with large escape values differences between libraries
#150
Bernadetadad
closed
11 months ago
0
minimum max of escape slider should depend on functional effect value
#149
Bernadetadad
closed
1 year ago
1
Add slider to filter heat-maps based on escape_std
#148
Bernadetadad
closed
1 year ago
2
fix zero count target bug in `analyze_variant_counts`
#147
jbloom
closed
1 year ago
0
Zero division error in rule `analyze_variant_counts`
#146
fwelsh
closed
1 year ago
1
add antibody count thresholds for prob escape (becomes version 2.4.0)
#145
jbloom
closed
1 year ago
0
post-selection barcode count filter
#144
Bernadetadad
closed
1 year ago
6
enable choice of neutralization standard (becomes version 2.3.0)
#143
jbloom
closed
1 year ago
0
fix bug in `analyze_variant_counts` when 0 count neut standards (becomes version 2.2.1)
#142
jbloom
closed
1 year ago
0
Accommodate multiple options for neut_std_barcode source
#141
fwelsh
closed
1 year ago
2
Error when any neut standard barcodes have 0 counts
#140
fwelsh
closed
1 year ago
3
add option to set `epitope_colors` in `polyclonal_config`
#139
jbloom
closed
1 year ago
0
Epitope color change
#138
Bernadetadad
closed
1 year ago
1
update to `polyclonal` 5.1 and `altair` 5.0.0rc1
#137
jbloom
closed
1 year ago
0
Server error: Forbidden when opening jupyter notebooks in updated dms-vep-pipeline environment
#136
fwelsh
closed
1 year ago
4
Update to `polyclonal` version 5.0
#135
jbloom
closed
1 year ago
0
separate `conda` env for `align_parse_PacBio_ccs`
#134
jbloom
closed
1 year ago
0
update to `polyclonal` 4.1 (becomes `dms-vep-pipeline` 2.0.1)
#133
jbloom
closed
1 year ago
0
update to `polyclonal` 4.0 (becomes `dms-vep-pipeline` version 2.0.0)
#132
jbloom
closed
1 year ago
0
fix bug in epitope harmonization (version 1.8.1)
#131
jbloom
closed
1 year ago
0
avg_antibody_escape.ipynb always makes one epitope average models
#130
caelanradford
closed
1 year ago
0
RuleException in rule avg_muteffects
#129
Bernadetadad
closed
1 year ago
1
Add legend for filtering dues to deleterious effect
#128
Bernadetadad
closed
11 months ago
2
update to `polyclonal` 3.4 (becomes `dms-vep-pipeline` 1.8.0)
#127
jbloom
closed
1 year ago
1
better handling of null values in muteffect heatmaps
#126
jbloom
closed
1 year ago
0
add `prebuilt_muteffects` option
#125
jbloom
closed
1 year ago
0
Functional score scale
#124
Bernadetadad
closed
1 year ago
5
pre-built functional scores
#123
jbloom
closed
1 year ago
3
fix bug in using pre-built variants with no `pacbio_runs`
#122
jbloom
closed
1 year ago
0
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