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MSKCC-Epi-Bio
/
gnomeR
Package to wrangle and visualize genomic data in R
https://mskcc-epi-bio.github.io/gnomeR/
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reference page for pathways() needs updating
#249
hfuchs5
closed
1 year ago
1
Potential option to make pathways() mutually exclusive
#248
hfuchs5
closed
1 year ago
1
test issue
#247
carokos
closed
1 year ago
0
Investigate genes with hyphen in their names. Are they 3 genes fused together?
#246
hfuchs5
closed
1 year ago
2
IMPACT vignette
#245
karissawhiting
closed
1 year ago
0
Update error messages for blank mutations and samples selected
#244
karissawhiting
closed
1 year ago
1
Pathways2
#243
karissawhiting
closed
1 year ago
0
dark theme R messages are hard to read
#242
hfuchs5
closed
1 year ago
1
sample ID shouldn't be required when passing to tbl_genomic()
#241
karissawhiting
closed
1 year ago
1
Make warnings for blank mutation status more specific
#240
karissawhiting
closed
1 year ago
0
Better Error Message when sample ids passed to samples arg are not in data in create_gene_binary()
#239
karissawhiting
closed
1 year ago
0
Purr when fix
#238
hfuchs5
closed
1 year ago
0
added better error messages for sample_id error
#237
hfuchs5
closed
1 year ago
0
added better error messages for sample_id error
#236
michaelcurry1123
closed
1 year ago
3
Updates to `add_pathways()` function
#235
carokos
closed
1 year ago
1
Misc clean up
#234
michaelcurry1123
closed
1 year ago
2
dat_oncoprint() function
#233
slb2240
closed
1 year ago
1
Clean out old data sets
#232
karissawhiting
closed
1 year ago
0
Colorblind color palette
#231
karissawhiting
opened
1 year ago
8
make function to reset set_gnomer_palette
#230
michaelcurry1123
closed
1 year ago
0
helper function to recode old fusion format to new format
#229
hfuchs5
closed
1 year ago
2
Update specify panel argument
#228
karissawhiting
closed
1 year ago
0
Edit vignette
#227
hfuchs5
closed
1 year ago
0
add error about specify panel variable names
#226
hfuchs5
closed
1 year ago
0
Allow users to pass alternate alias reference tables to recode_alias()
#225
karissawhiting
closed
1 year ago
2
putting recoded cna character amp/del values into pivot_cna_wider() returns numeric values
#224
hfuchs5
opened
1 year ago
1
remove packages from description
#223
michaelcurry1123
closed
1 year ago
1
Color pal
#222
michaelcurry1123
closed
1 year ago
7
Fix bug in pivot_cna_longer and add option for CNA high level only
#221
karissawhiting
closed
1 year ago
4
Which panel testing edits
#220
hfuchs5
closed
1 year ago
1
Testing annotate panel
#219
hfuchs5
closed
1 year ago
0
specifying impact panel doesn't seem to put fusion suffix on gene binary
#218
hfuchs5
closed
1 year ago
1
update sanitize mutations error and tests
#217
hfuchs5
closed
1 year ago
0
Move seg stuff
#216
karissawhiting
closed
1 year ago
0
GENIE BPC vignette
#215
hfuchs5
closed
1 year ago
2
Clean out old data sets
#214
karissawhiting
closed
1 year ago
0
Troubleshoot genie genes. Should this be added ?
#213
karissawhiting
closed
1 year ago
2
Add helper function to paste/remove endings on gene names (.Amp, .fus etc)
#212
karissawhiting
closed
1 year ago
4
Review color palette functions/objects
#211
karissawhiting
closed
1 year ago
2
Review Segmentation Functions
#210
karissawhiting
opened
1 year ago
1
Fusion processing
#209
karissawhiting
closed
1 year ago
0
which impact panel- show panels that gene is not on
#208
karissawhiting
closed
1 year ago
0
Outstanding cBioPortal Data Questions
#207
karissawhiting
opened
1 year ago
0
Website updates
#206
karissawhiting
closed
1 year ago
0
tidy process binary doesn't subset if samples provided
#205
hfuchs5
closed
1 year ago
0
error message should be removed or changed `summarize_by_gene()`?
#204
michaelcurry1123
closed
1 year ago
3
`purrr::when()` will be depreciated
#203
michaelcurry1123
closed
1 year ago
3
Internal gen bin tidy
#202
michaelcurry1123
closed
1 year ago
0
Check other functions that may be affected by sample ID column
#201
karissawhiting
closed
1 year ago
3
Review remaining arguments in `create_gene_binary()` and move `specify_panel` explanation to details in docs
#200
karissawhiting
closed
1 year ago
0
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