issues
search
DASL-Lab
/
provoc
PROportions of Variants of Concern using counts, coverage, and a variant matrix.
https://dasl-lab.github.io/provoc/
MIT License
0
stars
0
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
`plot_lineage_defs()` doesn't apply colours if all mutations match
#53
DBecker7
opened
3 months ago
0
Simplify the array of plotting functions.
#52
DBecker7
opened
4 months ago
0
Plotting functions should return the data in a plot friendly format.
#51
DBecker7
opened
4 months ago
0
Don't fail if one sample fails
#50
DBecker7
closed
4 months ago
1
`lineage_definition` class
#49
DBecker7
closed
4 months ago
1
Visualize `lineage_def` matrix (and pairwise matrix visualization)
#48
DBecker7
closed
4 months ago
3
pkgdown documentation
#47
DBecker7
closed
4 months ago
1
Refactor to reasonable names (incl. "lineage" rather than "variant")
#46
DBecker7
closed
4 months ago
1
plot.provoc should plot a time series if date_col specified.
#45
DBecker7
opened
5 months ago
0
Double check the mutations in `astronomize()`
#44
DBecker7
closed
4 months ago
1
`select_mutations()` function
#43
DBecker7
closed
5 months ago
1
Superfunction to run different model specs
#42
DBecker7
opened
5 months ago
2
Added support for all variant in mutation def selection for formula
#41
danerkestey
closed
5 months ago
0
preliminary feedback
#40
davidchampredon
opened
5 months ago
0
Additional documentation
#39
danerkestey
closed
5 months ago
0
34 `predict.provoc` to work with new data
#38
danerkestey
opened
5 months ago
0
Bootstrapping fully implemented
#37
DBecker7
closed
5 months ago
1
`plot.provoc` that generates a bar graph of proportions of VOC's
#36
danerkestey
closed
5 months ago
0
`Autoplot.provoc` implementation, similar to base R `plot.provoc`, using ggplot
#35
danerkestey
closed
5 months ago
0
`predict.provoc` to work with new data
#34
danerkestey
opened
5 months ago
0
Allow for "." notation in formula
#33
DBecker7
closed
5 months ago
0
More concise verbosity in `fuse()`
#32
DBecker7
closed
5 months ago
1
`by` argument should retain columns with constant information
#31
DBecker7
closed
5 months ago
0
`autoplot.provoc()` function
#30
DBecker7
closed
5 months ago
0
`plot.provoc()` function
#29
DBecker7
closed
5 months ago
0
Update all documentation to match current main branch implementation
#28
DBecker7
closed
5 months ago
0
mutation_col should check rows as well
#27
DBecker7
closed
5 months ago
0
Similarity of Variants (before and after data)
#26
DBecker7
opened
6 months ago
2
Simple Implementations of Freyja and Alcov models with unit tests
#25
danerkestey
opened
6 months ago
2
Gather more variant definitions and helper functions
#24
DBecker7
opened
6 months ago
1
Update Readme file
#23
DBecker7
closed
5 months ago
1
Identical variants after combining with data
#22
DBecker7
closed
5 months ago
0
Provoc Class Refactor
#21
danerkestey
closed
5 months ago
0
Enhance `provoc` with GLM and Flexible Data Handling
#20
danerkestey
closed
6 months ago
1
Update parse_mutations.R
#19
danerkestey
closed
7 months ago
2
13 implement predictprovoc method
#18
danerkestey
closed
7 months ago
1
Investigate the effect of changes to the variant matrix (variable importance measures)
#17
DBecker7
opened
8 months ago
0
Investigate the usefulness of GLM standard errors
#16
DBecker7
opened
8 months ago
0
Documentation inheritance
#15
DBecker7
closed
5 months ago
2
Implement `provoc` class (S3)
#14
DBecker7
closed
5 months ago
1
Implement `predict.provoc` method
#13
DBecker7
closed
7 months ago
1
Implement simple versions of Freyja and/or Alcov for comparison
#12
DBecker7
opened
8 months ago
0
Fix bootstrapping code
#11
DBecker7
closed
6 months ago
2
Create a repo logo
#10
DBecker7
closed
6 months ago
1
Add example data
#9
DBecker7
closed
8 months ago
0
Create a vignette
#8
DBecker7
closed
8 months ago
1
Re-write `provoc_optim` in C++ (if possible)
#7
DBecker7
closed
5 months ago
1
Define `summary` and `plot` methods for objects of class `provoc`.
#6
DBecker7
closed
5 months ago
1
Add unit tests
#5
DBecker7
opened
8 months ago
1
Faster `parse_unique_mutations` function
#4
DBecker7
closed
7 months ago
1
Next