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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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Add IH3 & IH4 panels
#299
jalavery
closed
1 year ago
0
AM_Hck_testbinary
#298
akriti21
closed
11 months ago
1
Copy Number Alteration Vignette
#297
alrein-05
opened
1 year ago
1
Tests for tbl_genomic
#296
jflynn264
closed
1 year ago
0
Update GENIE-vignette.Rmd
#295
slb2240
closed
1 year ago
1
gene_binary duplicated IDs
#294
jflynn264
opened
1 year ago
6
Minor bugs in `create_gene_binary()`
#293
akriti21
opened
1 year ago
4
Update tbl genomic
#292
alrein-05
closed
1 year ago
0
Testing sanitize data functions
#291
whitec4
closed
1 year ago
0
Add function subset_by_panel and unit tests
#290
jalavery
closed
1 year ago
1
add_pathways() updates and tests
#289
jflynn264
closed
1 year ago
0
create internal paste/remove endings function
#288
whitec4
closed
1 year ago
0
Gb class internal func
#287
hfuchs5
opened
1 year ago
1
Update Pathways Functions
#286
karissawhiting
closed
1 year ago
0
create function to check for new class
#285
hfuchs5
closed
1 year ago
1
Update Messages and Warnings in create_gene_binary()
#284
hfuchs5
closed
1 year ago
0
Genie vignette
#283
hfuchs5
closed
1 year ago
0
downsize number of datasets
#282
hfuchs5
closed
11 months ago
0
update genie branch
#281
hfuchs5
closed
1 year ago
0
Add internal function to check binary matrix inputs
#280
karissawhiting
opened
1 year ago
0
Update tbl_genomic() and remove gene prevalence arguments
#279
karissawhiting
closed
1 year ago
0
Check warnings/info returned from create_gene_binary
#278
karissawhiting
closed
11 months ago
1
text matrix
#277
michaelcurry1123
closed
1 year ago
0
Create GENIE BPC vignette
#276
slb2240
closed
1 year ago
0
merge in main changes
#275
hfuchs5
closed
1 year ago
0
Fusion format function
#274
hfuchs5
closed
1 year ago
11
Add subset_by_panel() function
#273
karissawhiting
closed
1 year ago
2
merge in main commits
#272
hfuchs5
closed
1 year ago
0
merge in main
#271
hfuchs5
closed
1 year ago
0
Alt freq functions
#270
karissawhiting
closed
1 year ago
0
Check how point mutations or genes with a period are treated
#269
karissawhiting
closed
1 year ago
4
allow custom alias tables to be provided
#268
hfuchs5
closed
1 year ago
1
pull main changes
#267
hfuchs5
closed
1 year ago
0
Faster summarize by gene
#266
hfuchs5
closed
1 year ago
3
Cna vignette
#265
alrein-05
closed
1 year ago
2
Merge main
#264
hfuchs5
closed
1 year ago
0
Create text binary matrix which retains specific mutation type in matrix
#263
karissawhiting
opened
1 year ago
16
Create function to subset binary matrix by percentage cutoff
#262
karissawhiting
closed
1 year ago
0
Create function to subset binary matrix by percentage cutoff
#261
karissawhiting
closed
1 year ago
1
Small fixes from Caroline's review
#260
karissawhiting
closed
1 year ago
0
summarize_by_gene VERY slow
#259
hfuchs5
closed
1 year ago
5
Create a vignette for copy number data
#258
hfuchs5
opened
1 year ago
0
Add an example to vignette and/or docs that changes color palette of the ggcor or ggcomut plot
#257
hfuchs5
opened
1 year ago
2
Improve documentation and color defaults for ggcomut
#256
hfuchs5
opened
1 year ago
1
Allow users to select specific genes in ggcor (or add example of preselecting genes)
#255
hfuchs5
opened
1 year ago
0
vignette edits needed
#254
hfuchs5
closed
1 year ago
1
tbl_genomic: freq_cutoff issue
#253
hfuchs5
closed
1 year ago
6
create_gene_binary: confusing documentation
#252
hfuchs5
closed
1 year ago
1
count_pathways_by() has confusing documentation and functionality regarding gene level vs. alt level
#251
hfuchs5
closed
1 year ago
3
SMALL fix: pathways() custom_pathways argument documentation
#250
hfuchs5
closed
1 year ago
1
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