umccr/RNAsum

Issues

• Tasks to address when adding option to use“full” TCGA reference cohort

  #164 opened 4 months ago by JMarzec
  0

• Consider introducing negation flags

  #163 opened 4 months ago by skanwal
  0

• Handle missing `plot_legend1` in `data_transformation_plot` else condition

  #161 opened 4 months ago by pdiakumis
  0

• Update description for z-score plots

  #157 opened 5 months ago by skanwal
  2

• Filtered normalised genes

  #158 opened 5 months ago by skanwal
  0

• Fix order of Arriba plots displayed in the report output from Rpackage

  #153 opened 6 months ago by skanwal
  0

• Update cancer gene list used in the Rpackage

  #154 opened 6 months ago by skanwal
  0

• Check for missing RNA fusions with DNA support

  #152 opened 6 months ago by skanwal
  0

• Handle Manta SV without fusions

  #145 opened 9 months ago by pdiakumis
  1

• Error in `grid.newpage()`: could not open file

  #147 opened 9 months ago by pdiakumis
  2

• Update links to PURPLE

  #56 opened a year ago by skanwal
  1

• Circos table not showing up

  #132 opened 10 months ago by pdiakumis
  0

• manhattanly::manhattanr gene argument specified as Diff_Z_score but this column not found in 'x' data.frame

  #129 opened 10 months ago by pdiakumis
  0

• Empty fusion outputs not handled

  #112 opened 10 months ago by skanwal
  3

• Update Fusion Filtration

  #91 opened 10 months ago by pdiakumis
  1

• no 'dimnames' attribute for array

  #131 opened 10 months ago by skanwal
  1

• update readme for r-package

  #142 opened 10 months ago by skanwal
  0

• Consider removing immune section

  #141 opened 10 months ago by skanwal
  0

• Library size plot: add patient label

  #140 opened 10 months ago by pdiakumis
  0

• Consider Simplified RNAsum reporter

  #139 opened 10 months ago by pdiakumis
  0

• DB: Ingest Fusions

  #138 opened 10 months ago by pdiakumis
  0

• Add support for transcript level counts in R-package code

  #137 opened 10 months ago by skanwal
  0

• Update Ensembl

  #86 opened a year ago by pdiakumis
  2

• Debug: Duplicate fusions

  #134 opened a year ago by skanwal
  0

• Consider rounding expression values

  #123 opened a year ago by pdiakumis
  0

• Handle sash SV file

  #126 opened a year ago by pdiakumis
  0

• exprGroupsStats_geneWise.R: Subscript out of bounds

  #122 opened a year ago by pdiakumis
  1

• Failed clinical sample

  #109 opened a year ago by skanwal
  6

• Handle new ensembl gene annotations

  #110 opened a year ago by skanwal
  3

• Potential issue for samples with few fusions and/or low expression / few pcgr entries

  #78 opened a year ago by MonicaSolbakken
  2

• Upgrade bioconductor version

  #100 opened a year ago by alexiswl
  1

• Warning when executing gene_annot_processed_data_save chunk

  #50 opened a year ago by skanwal
  1

• Use {conflicted} for R pkg conflict resolution

  #87 opened a year ago by pdiakumis
  1

• Merge duplicated CGI known translocations

  #89 opened a year ago by pdiakumis
  2

• R package structure pointers

  #57 opened a year ago by pdiakumis
  1

• Update pkgdown website

  #105 opened a year ago by pdiakumis
  1

• Build manhattanly conda dependency

  #106 opened a year ago by pdiakumis
  1

• Set up conda package

  #104 opened a year ago by pdiakumis
  1

• Keep reference data in separate R data package

  #108 opened a year ago by pdiakumis
  0

• Replace Carriage Return (`^M`) in reference `Target.txt` files

  #67 opened a year ago by pdiakumis
  1

• Github Actions fails at Create and Push Manifest File step of tag_manifest job

  #98 opened 2 years ago by alexiswl
  0

• Missing Fusion Handling

  #90 opened 2 years ago by pdiakumis
  1

• exprTable: use unique cuts/values for DT styleInterval

  #93 opened 2 years ago by pdiakumis
  1

• Test data quitting from lines 1856-2194 - attempt to set an attribute on NULL

  #75 opened 2 years ago by MonicaSolbakken
  2

• Missed gene expression - DLL3

  #73 opened 2 years ago by skanwal
  1

• Missed gene expression - CTCF

  #74 opened 2 years ago by skanwal
  1

• Missed fusion output

  #68 opened 2 years ago by skanwal
  1

• argument is of length zero

  #70 opened 2 years ago by skanwal
  1

• Current docker build fails with conda dep/conflicts error

  #53 opened 3 years ago by alexiswl
  1

• Error report regarding to "fusions_filtering" at when only Dragen RNA fusion callings are available

  #49 opened 3 years ago by senzhaocode
  4