morinlab/GAMBLR.data

Issues

• GAMBLR.data optimization for get_ssm_by_regions

  #89 opened 2 months ago by Kdreval
  0

• The disconnect between 2 bundled metadata objects

  #85 opened 3 months ago by Kdreval
  0

• Duplicate sample ids in the metadata

  #81 opened 5 months ago by vladimirsouza
  1

• setup all ssm functions to support study subsetting

  #77 opened 6 months ago by Kdreval
  1

• Setup metadata to support `case_set` argument

  #76 opened 6 months ago by Kdreval
  1

• Bundle DLBCL Trios with GAMBLR.data

  #66 opened 6 months ago by Kdreval
  1

• Add HNRNPU to aSHM region list

  #75 opened 6 months ago by Kdreval
  2

• The badge README.md doesn't show up

  #78 opened 6 months ago by vladimirsouza
  1

• Bundle Arthur et al with GAMBLR.data

  #65 opened 6 months ago by Kdreval
  2

• Github actions for GAMBLR.data

  #67 opened 6 months ago by Kdreval
  1

• README is outdated

  #68 opened 6 months ago by Kdreval
  1

• cyclic dependency

  #70 opened 6 months ago by Kdreval
  2

• missing dataset documentation

  #71 opened 6 months ago by Kdreval
  1

• missing documentation

  #72 opened 6 months ago by Kdreval
  1

• tests need to be dropped or modified

  #73 opened 6 months ago by Kdreval
  2

• Add function `get_cnv_and_ssm_status`

  #57 opened 8 months ago by vladimirsouza
  2

• `sample_data[[projection]]$ashm` misses `RefSeq` column

  #62 opened 7 months ago by vladimirsouza
  0

• get_ashm_counts_matrix is missing check for provided maf data

  #61 opened 7 months ago by Kdreval
  0

• Create GAMBLR.data version of `get_ashm_count_matrix`

  #59 opened 7 months ago by Kdreval
  1

• get_coding_ssm_status is missing some features

  #58 opened 7 months ago by rdmorin
  4

• Finish GAMBLR child repos and update documentation

  #54 opened 8 months ago by rdmorin
  3

• The Pipeline column of bundled variant calls is not up-to-date

  #52 opened 8 months ago by Kdreval
  1

• bundling ashm data with the package

  #51 opened 8 months ago by Kdreval
  1

• Discrepancies in how the two objects grch37_gene_coordinates and hg38_gene_coordinates are compiled.

  #48 opened 9 months ago by mattssca
  0

• Bug in get_ssm_by_sample

  #46 opened 9 months ago by mattssca
  0

• ashm data frames have inconsistent chr prefixing

  #11 opened a year ago by lkhilton
  1

• Function import tags vs. in-code package prefixing

  #44 opened 10 months ago by mattssca
  0

• Documentation for bundled metadata

  #21 opened 10 months ago by mattssca
  0

• Add DLBCL cell lines data to bundled sample_data

  #41 opened 10 months ago by Kdreval
  1

• AICDA is misspelled in aSHM sites (v0.4)

  #39 opened 10 months ago by Kdreval
  0

• maf_data is not a valid parameter for GAMBLR.data::get_ssm_by_region

  #37 opened 10 months ago by mattssca
  1

• GAMBLR.data and GAMBLR.results versions of `get_ssm_by_regions` may return different outputs when `basic_columns = TRUE`

  #33 opened a year ago by vladimirsouza
  1

• Documentation for mirage_metrics

  #29 opened a year ago by mattssca
  1

• Discrepancies in "Lymph Gen" column names between the two bundled metadata objects.

  #24 opened a year ago by mattssca
  6

• No documentation for the bundled data sets

  #9 opened a year ago by mattssca
  0

• Bundle BL data

  #14 opened a year ago by Kdreval
  1

• Bundle FL data

  #15 opened a year ago by Kdreval
  1

• Bundle DLBCL data

  #16 opened a year ago by Kdreval
  2

• Consider adding complete examples that details how any additional data is retrieved.

  #6 opened a year ago by mattssca
  1

• Object 'colour_codes' not found

  #7 opened a year ago by mattssca
  1

• Version parameter description is missing from get_genes

  #8 opened a year ago by mattssca
  1

• Inconsistencies with the spelling of "ensembl"

  #5 opened a year ago by mattssca
  1