DASL-Lab provoc issues - Githubissues

DASL-Lab / provoc

PROportions of Variants of Concern using counts, coverage, and a variant matrix.

https://dasl-lab.github.io/provoc/

MIT License

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`plot_lineage_defs()` doesn't apply colours if all mutations match

#53 DBecker7 opened 1 month ago
0
Simplify the array of plotting functions.

#52 DBecker7 opened 2 months ago
0
Plotting functions should return the data in a plot friendly format.

#51 DBecker7 opened 2 months ago
0
Don't fail if one sample fails

#50 DBecker7 closed 2 months ago
1
`lineage_definition` class

#49 DBecker7 closed 2 months ago
1
Visualize `lineage_def` matrix (and pairwise matrix visualization)

#48 DBecker7 closed 2 months ago
3
pkgdown documentation

#47 DBecker7 closed 2 months ago
1
Refactor to reasonable names (incl. "lineage" rather than "variant")

#46 DBecker7 closed 2 months ago
1
plot.provoc should plot a time series if date_col specified.

#45 DBecker7 opened 3 months ago
0
Double check the mutations in `astronomize()`

#44 DBecker7 closed 2 months ago
1
`select_mutations()` function

#43 DBecker7 closed 3 months ago
1
Superfunction to run different model specs

#42 DBecker7 opened 3 months ago
2
Added support for all variant in mutation def selection for formula

#41 danerkestey closed 3 months ago
0
preliminary feedback

#40 davidchampredon opened 3 months ago
0
Additional documentation

#39 danerkestey closed 3 months ago
0
34 `predict.provoc` to work with new data

#38 danerkestey opened 3 months ago
0
Bootstrapping fully implemented

#37 DBecker7 closed 3 months ago
1
`plot.provoc` that generates a bar graph of proportions of VOC's

#36 danerkestey closed 3 months ago
0
`Autoplot.provoc` implementation, similar to base R `plot.provoc`, using ggplot

#35 danerkestey closed 3 months ago
0
`predict.provoc` to work with new data

#34 danerkestey opened 3 months ago
0
Allow for "." notation in formula

#33 DBecker7 closed 3 months ago
0
More concise verbosity in `fuse()`

#32 DBecker7 closed 3 months ago
1
`by` argument should retain columns with constant information

#31 DBecker7 closed 3 months ago
0
`autoplot.provoc()` function

#30 DBecker7 closed 3 months ago
0
`plot.provoc()` function

#29 DBecker7 closed 3 months ago
0
Update all documentation to match current main branch implementation

#28 DBecker7 closed 3 months ago
0
mutation_col should check rows as well

#27 DBecker7 closed 3 months ago
0
Similarity of Variants (before and after data)

#26 DBecker7 opened 4 months ago
2
Simple Implementations of Freyja and Alcov models with unit tests

#25 danerkestey opened 4 months ago
2
Gather more variant definitions and helper functions

#24 DBecker7 opened 4 months ago
1
Update Readme file

#23 DBecker7 closed 3 months ago
1
Identical variants after combining with data

#22 DBecker7 closed 3 months ago
0
Provoc Class Refactor

#21 danerkestey closed 3 months ago
0
Enhance `provoc` with GLM and Flexible Data Handling

#20 danerkestey closed 5 months ago
1
Update parse_mutations.R

#19 danerkestey closed 5 months ago
2
13 implement predictprovoc method

#18 danerkestey closed 5 months ago
1
Investigate the effect of changes to the variant matrix (variable importance measures)

#17 DBecker7 opened 6 months ago
0
Investigate the usefulness of GLM standard errors

#16 DBecker7 opened 6 months ago
0
Documentation inheritance

#15 DBecker7 closed 3 months ago
2
Implement `provoc` class (S3)

#14 DBecker7 closed 3 months ago
1
Implement `predict.provoc` method

#13 DBecker7 closed 5 months ago
1
Implement simple versions of Freyja and/or Alcov for comparison

#12 DBecker7 opened 6 months ago
0
Fix bootstrapping code

#11 DBecker7 closed 4 months ago
2
Create a repo logo

#10 DBecker7 closed 4 months ago
1
Add example data

#9 DBecker7 closed 6 months ago
0
Create a vignette

#8 DBecker7 closed 6 months ago
1
Re-write `provoc_optim` in C++ (if possible)

#7 DBecker7 closed 3 months ago
1
Define `summary` and `plot` methods for objects of class `provoc`.

#6 DBecker7 closed 3 months ago
1
Add unit tests

#5 DBecker7 opened 6 months ago
1
Faster `parse_unique_mutations` function

#4 DBecker7 closed 5 months ago
1