Issues

• Empty string gene symbols in SV data create spurious .fus column in create_gene_binary()

  MSKCC-Epi-Bio/gnomeR#356 · Filter by author karissawhiting opened on Jun 17, 2026

• Add missing panel from AACR Project GENIE public version 17_0

  MSKCC-Epi-Bio/gnomeR#354 · Filter by author MOOKY7 opened on May 16, 2025

• .select_to_varnames() and .formula_list_to_named_list() to be deprecated

  MSKCC-Epi-Bio/gnomeR#348 · Filter by author ddsjoberg opened on Aug 23, 2024

• Add summarize_by_patient() function

  MSKCC-Epi-Bio/gnomeR#345 · Filter by author karissawhiting opened on Jun 27, 2024

• add unit testing for add_point_mut()

  MSKCC-Epi-Bio/gnomeR#343 · Filter by author hfuchs5 opened on May 9, 2024

• Update Docs to make sure new SV is canon-cbio has deprecated fusion files for sv

  MSKCC-Epi-Bio/gnomeR#338 · Filter by author hfuchs5 opened on Nov 9, 2023

• unit testing for tbl_genomic(..., wide = T) needed

  MSKCC-Epi-Bio/gnomeR#337 · Filter by author hfuchs5 opened on Nov 9, 2023
  1

• unit testing for mutation type attribute on create_gene_binary()

  MSKCC-Epi-Bio/gnomeR#336 · Filter by author hfuchs5 opened on Nov 2, 2023
  

• Large datasets (1,000s of patients) takes a long time in summarize_by_gene()

  MSKCC-Epi-Bio/gnomeR#329 · Filter by author hfuchs5 opened on Oct 22, 2023
  

• Check how vdiffr is counted for code coverage in tests

  MSKCC-Epi-Bio/gnomeR#327 · Filter by author karissawhiting opened on Oct 5, 2023
  

• Add annotation of point mutations in create gene binary pipeline

  ready for review
  MSKCC-Epi-Bio/gnomeR#322 · Filter by author karissawhiting opened on Aug 31, 2023
  3

  

• cbio vs synapse GENIE BPC data fusion discrepancy in names

  future
  MSKCC-Epi-Bio/gnomeR#312 · Filter by author hfuchs5 opened on Jun 20, 2023

• "LOSS" not accepted as an alteration type for pivot_cna_wider

  pre-hackathon
  MSKCC-Epi-Bio/gnomeR#309 · Filter by author hfuchs5 opened on Jun 15, 2023
  1

  

• Allow subset_by_frequency to calculate and subset by group frequency

  enhancementhackathon
  MSKCC-Epi-Bio/gnomeR#305 · Filter by author karissawhiting opened on May 16, 2023

• gene_binary duplicated IDs

  pre-hackathon
  MSKCC-Epi-Bio/gnomeR#294 · Filter by author jflynn264 opened on Apr 27, 2023
  6

  

• Minor bugs in create_gene_binary()

  pre-hackathon
  MSKCC-Epi-Bio/gnomeR#293 · Filter by author akriti21 opened on Apr 27, 2023
  4

  

• Add internal function to check binary matrix inputs

  cranfuture
  MSKCC-Epi-Bio/gnomeR#280 · Filter by author karissawhiting opened on Apr 4, 2023
  

• Create text binary matrix which retains specific mutation type in matrix

  ready for review
  MSKCC-Epi-Bio/gnomeR#263 · Filter by author karissawhiting opened on Feb 21, 2023
  16

  

• Create a vignette for copy number data

  hackathon
  MSKCC-Epi-Bio/gnomeR#258 · Filter by author hfuchs5 opened on Feb 14, 2023 · Caroline Review of v1.2.0
  

• Add an example to vignette and/or docs that changes color palette of the ggcor or ggcomut plot

  hackathon
  MSKCC-Epi-Bio/gnomeR#257 · Filter by author hfuchs5 opened on Feb 14, 2023 · Caroline Review of v1.2.0
  2

• Improve documentation and color defaults for ggcomut

  hackathon
  MSKCC-Epi-Bio/gnomeR#256 · Filter by author hfuchs5 opened on Feb 14, 2023 · Caroline Review of v1.2.0
  1

  

• Allow users to select specific genes in ggcor (or add example of preselecting genes)

  MSKCC-Epi-Bio/gnomeR#255 · Filter by author hfuchs5 opened on Feb 14, 2023 · Caroline Review of v1.2.0

• Colorblind color palette

  hackathon
  MSKCC-Epi-Bio/gnomeR#231 · Filter by author karissawhiting opened on Dec 13, 2022
  8

• putting recoded cna character amp/del values into pivot_cna_wider() returns numeric values

  MSKCC-Epi-Bio/gnomeR#224 · Filter by author hfuchs5 opened on Dec 5, 2022
  1

• Review Segmentation Functions

  MSKCC-Epi-Bio/gnomeR#210 · Filter by author karissawhiting opened on Nov 15, 2022
  1