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dms-vep
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dms-vep-pipeline-3
Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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allow non-alphanumeric characters in summary keys
#112
Bernadetadad
closed
8 months ago
1
lint Jupyter notebooks by fixing `ruff.toml`
#111
jbloom
closed
7 months ago
0
enable generation of multiple distinctly configured summary plots
#110
jbloom
closed
7 months ago
1
add example on per-condition filters for func effect diffs (addresses #108)
#109
jbloom
closed
9 months ago
0
Add an option to filter functional difference heatmaps based on functional scores
#108
Bernadetadad
closed
9 months ago
1
"minimum max" filter bug
#107
Bernadetadad
opened
9 months ago
3
fix `.gitignore` in test example
#106
jbloom
closed
9 months ago
0
Add single nucleotide accessibility to heatmaps
#105
Bernadetadad
closed
7 months ago
0
gitignore wrong file name
#104
Bernadetadad
closed
9 months ago
0
pipeline runs when `antibody_escape_config` is `null`
#103
jbloom
closed
9 months ago
0
Pipeline not running without antibody escape
#102
arjunaditham
closed
9 months ago
8
better error messages when problems with `barcode_runs`
#101
jbloom
closed
10 months ago
0
snakemake issue with the latest environment update
#100
Bernadetadad
closed
10 months ago
2
add `func_effect_diffs` rule
#99
jbloom
closed
10 months ago
0
update environment
#98
jbloom
closed
10 months ago
0
Add functional scores to multidms heatmaps
#97
Bernadetadad
closed
10 months ago
1
filtering low effect mutants in heatmaps for receptor binding and mAb escape
#96
bblarsen-sci
closed
10 months ago
1
Periodic Wildcard Error
#95
jbloom
closed
10 months ago
0
constrain `{chart}` wildcard in `format_altair`
#94
jbloom
closed
10 months ago
0
move model instantiation inside loop
#93
jgallowa07
closed
10 months ago
3
`multidms` fitting bug in func_effect_shifts.ipynb
#92
jgallowa07
closed
10 months ago
3
86 1 multidms softplus clipping
#91
jgallowa07
closed
5 months ago
8
site highlighting broken in summary plots
#90
jbloom
closed
1 year ago
2
Fix bug in reporting pre-selection counts cutoff in `func_scores`
#89
jbloom
closed
1 year ago
0
Fix bug in reporting pre-selection counts cutoff in `func_scores`
#88
jbloom
closed
1 year ago
0
Issue with displaying cutoff in 'analyze_func_scores'
#87
bblarsen-sci
closed
1 year ago
1
Updating `multidms` fitting
#86
jgallowa07
opened
1 year ago
11
Fix bug in `per_antibody_escape.csv` production in `summary` introduced in version 3.5.1.
#85
jbloom
closed
1 year ago
0
Fix bug introduced in `summary` when no antibodies in version 3.5.1
#84
jbloom
closed
1 year ago
0
`summary` rule creates `per_antibody_escape.csv`
#83
jbloom
closed
1 year ago
0
fix tooltips in columns with `.` in name
#82
jbloom
closed
1 year ago
0
In 'std_chart', sometimes tooltip doesn't show individual values, but instead shows NaN
#81
bblarsen-sci
closed
1 year ago
1
allow customization of x-axis in prob escape plots
#80
jbloom
closed
1 year ago
0
filter noisy measurements with high standard deviations
#79
jbloom
closed
1 year ago
0
enable filtering of measurements that are highly disparate among replicates
#78
jbloom
closed
1 year ago
1
Pipeline getting hung up near final steps
#77
bblarsen-sci
closed
1 year ago
5
added `baltic` to environment
#76
jbloom
closed
1 year ago
0
update `dmslogo` to 0.7.0 to fix #74
#75
jbloom
closed
1 year ago
0
Potential package version conflict with dmslogo?
#74
Caleb-Carr
closed
1 year ago
2
update `conda` env
#73
jbloom
closed
1 year ago
0
Allow to invert concentration scale
#72
Bernadetadad
closed
1 year ago
6
figure of mutation effects on cell entry by domain and mutation type, and correlation to natural evolution
#71
jbloom
closed
1 year ago
1
`summary` plots allow fixed limits
#70
jbloom
closed
1 year ago
0
add max_fixed to summary plots
#69
Bernadetadad
closed
1 year ago
1
Unknown javascript error in summary html plot
#68
Caleb-Carr
closed
1 year ago
4
Order antibodies in `summary` plots as ordered in config
#67
jbloom
closed
1 year ago
0
make summary plots customizable for antibody order
#66
bblarsen-sci
closed
1 year ago
1
Fix bug when `barcode_counts` set to `null`
#65
WillHannon-MCB
closed
1 year ago
0
Issue setting `barcode_runs` to `null`
#64
WillHannon-MCB
closed
1 year ago
1
Fix bug in `summary` when no `other_assays`; also fix filtering on heatmaps sliders when more than two other properties
#63
jbloom
closed
1 year ago
0
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