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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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Adding "by" parameter to subset_by_freqency() function
#349
toumban1
opened
2 weeks ago
0
`.select_to_varnames()` and `.formula_list_to_named_list()` to be deprecated
#348
ddsjoberg
opened
3 weeks ago
0
Integrate 2023 changes
#347
toumban1
opened
1 month ago
0
Add summarize by patient
#346
jalavery
opened
2 months ago
2
Add `summarize_by_patient()` function
#345
karissawhiting
opened
2 months ago
0
Point mutation documenation/function
#344
hfuchs5
opened
3 months ago
0
add unit testing for `add_point_mut()`
#343
hfuchs5
opened
4 months ago
0
Plottting function gene selection
#342
toumban1
opened
4 months ago
0
Add wide option to tbl_genomic()
#341
karissawhiting
opened
6 months ago
0
Reivew and Reorganize internals
#340
karissawhiting
closed
5 months ago
2
Add extract patient function
#339
karissawhiting
closed
9 months ago
1
Update Docs to make sure new SV is canon-cbio has deprecated fusion files for sv
#338
hfuchs5
opened
10 months ago
0
unit testing for tbl_genomic(..., wide = T) needed
#337
hfuchs5
opened
10 months ago
1
unit testing for mutation type attribute on `create_gene_binary()`
#336
hfuchs5
opened
10 months ago
0
Mutation type matrix for ggoncoprint retained after `create_gene_binary()`
#335
hfuchs5
opened
10 months ago
0
Seq freq group hackathon
#334
hfuchs5
closed
10 months ago
0
Add "by" variable to subset_by_frequency() and add unit tests
#333
hfuchs5
closed
10 months ago
0
Group freq subset
#332
hfuchs5
closed
10 months ago
1
Add function to extract patient ID from sample ID
#331
karissawhiting
closed
2 months ago
0
Add "by" variable to subset_by_frequency() and add unit tests
#330
toumban1
closed
10 months ago
1
Large datasets (1,000s of patients) takes a long time in `summarize_by_gene()`
#329
hfuchs5
opened
10 months ago
0
mutationStatus message issue fix
#328
hfuchs5
closed
8 months ago
1
Check how vdiffr is counted for code coverage in tests
#327
karissawhiting
opened
11 months ago
0
add other_vars arg to add_pathways and clean up code and docs
#326
karissawhiting
closed
11 months ago
0
Add `other_vars` arg to `add_pathways`
#325
karissawhiting
closed
11 months ago
0
Internal colname messages
#324
karissawhiting
closed
11 months ago
1
fix warning message and add test
#323
karissawhiting
closed
1 year ago
0
Add annotation of point mutations in create gene binary pipeline
#322
karissawhiting
opened
1 year ago
3
update to allow other vars in summarize
#321
hfuchs5
closed
1 year ago
1
create internal func and put in relevant funcs
#320
hfuchs5
closed
12 months ago
1
adding panels for GENIE specifications
#319
hfuchs5
closed
1 year ago
2
Incorrectly sending message that no samples have alterations
#318
hfuchs5
closed
1 year ago
1
update names processing underlying data
#317
karissawhiting
closed
1 year ago
0
fix pathways bug
#316
karissawhiting
closed
1 year ago
1
Pathways bug
#315
karissawhiting
closed
1 year ago
0
Wrong columns in error message
#314
karissawhiting
closed
12 months ago
1
Sample_ID not recognized as valid column name
#313
karissawhiting
closed
1 year ago
1
cbio vs synapse GENIE BPC data fusion discrepancy in names
#312
hfuchs5
opened
1 year ago
0
update index
#311
karissawhiting
closed
1 year ago
0
Warning message from summarize_by_gene()
#310
karissawhiting
closed
1 year ago
1
"LOSS" not accepted as an alteration type for pivot_cna_wider
#309
hfuchs5
opened
1 year ago
1
update genie aliases
#308
karissawhiting
closed
1 year ago
0
Tbl genomic wide
#307
slb2240
closed
4 months ago
1
`summarize_by_gene()` should allow `other_vars` argument
#306
karissawhiting
closed
12 months ago
2
Allow subset_by_frequency to calculate and subset by group frequency
#305
karissawhiting
opened
1 year ago
0
error message in create_gene_binary specify_panel argument should be warning
#304
hfuchs5
closed
1 year ago
1
reformat_fusion() doesn't properly clean the fusion data
#303
hfuchs5
closed
1 year ago
1
variant_classification error messaging
#302
jalavery
closed
11 months ago
0
add_pathways .mut ending requirement for custom pathway
#301
hfuchs5
closed
12 months ago
1
Added unit tests for gnomer-color-palette and plotting functions
#300
toumban1
closed
11 months ago
2
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