MSKCC-Epi-Bio gnomeR issues

MSKCC-Epi-Bio / gnomeR

Package to wrangle and visualize genomic data in R

https://mskcc-epi-bio.github.io/gnomeR/

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issues

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Add summarize by patient

#346 jalavery opened 4 days ago
0
Add `summarize_by_patient()` function

#345 karissawhiting opened 3 weeks ago
0
Point mutation documenation/function

#344 hfuchs5 opened 1 month ago
0
add unit testing for `add_point_mut()`

#343 hfuchs5 opened 2 months ago
0
Plottting function gene selection

#342 toumban1 opened 2 months ago
0
Add wide option to tbl_genomic()

#341 karissawhiting opened 4 months ago
0
Reivew and Reorganize internals

#340 karissawhiting closed 4 months ago
2
Add extract patient function

#339 karissawhiting closed 7 months ago
1
Update Docs to make sure new SV is canon-cbio has deprecated fusion files for sv

#338 hfuchs5 opened 8 months ago
0
unit testing for tbl_genomic(..., wide = T) needed

#337 hfuchs5 opened 8 months ago
1
unit testing for mutation type attribute on `create_gene_binary()`

#336 hfuchs5 opened 8 months ago
0
Mutation type matrix for ggoncoprint retained after `create_gene_binary()`

#335 hfuchs5 opened 8 months ago
0
Seq freq group hackathon

#334 hfuchs5 closed 8 months ago
0
Add "by" variable to subset_by_frequency() and add unit tests

#333 hfuchs5 closed 8 months ago
0
Group freq subset

#332 hfuchs5 closed 8 months ago
1
Add function to extract patient ID from sample ID

#331 karissawhiting closed 3 weeks ago
0
Add "by" variable to subset_by_frequency() and add unit tests

#330 toumban1 closed 8 months ago
1
Large datasets (1,000s of patients) takes a long time in `summarize_by_gene()`

#329 hfuchs5 opened 9 months ago
0
mutationStatus message issue fix

#328 hfuchs5 closed 7 months ago
1
Check how vdiffr is counted for code coverage in tests

#327 karissawhiting opened 9 months ago
0
add other_vars arg to add_pathways and clean up code and docs

#326 karissawhiting closed 9 months ago
0
Add `other_vars` arg to `add_pathways`

#325 karissawhiting closed 9 months ago
0
Internal colname messages

#324 karissawhiting closed 9 months ago
1
fix warning message and add test

#323 karissawhiting closed 10 months ago
0
Add annotation of point mutations in create gene binary pipeline

#322 karissawhiting opened 10 months ago
3
update to allow other vars in summarize

#321 hfuchs5 closed 10 months ago
1
create internal func and put in relevant funcs

#320 hfuchs5 closed 10 months ago
1
adding panels for GENIE specifications

#319 hfuchs5 closed 11 months 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 10 months 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 10 months ago
1
Sample_ID not recognized as valid column name

#313 karissawhiting closed 10 months 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 10 months 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 2 months ago
1
`summarize_by_gene()` should allow `other_vars` argument

#306 karissawhiting closed 10 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 10 months 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 9 months ago
0
add_pathways .mut ending requirement for custom pathway

#301 hfuchs5 closed 10 months ago
1
Added unit tests for gnomer-color-palette and plotting functions

#300 toumban1 closed 9 months ago
2
Add IH3 & IH4 panels

#299 jalavery closed 1 year ago
0
AM_Hck_testbinary

#298 akriti21 closed 10 months ago
1
Copy Number Alteration Vignette

#297 alrein-05 opened 1 year ago
1