Issues

• Heatmap output appears abnormal

  navinlabcode/copykat#141 · Filter by author TheSallyGardens opened on Jul 10, 2026
  1

• License discrepency

  navinlabcode/copykat#140 · Filter by author acruicks-tide opened on May 12, 2026

• Running copyKAT on large datasets

  navinlabcode/copykat#138 · Filter by author ManarRashad opened on Mar 12, 2026
  3

• Copykat for Single cell Flex

  navinlabcode/copykat#137 · Filter by author rebekahdadey opened on Mar 10, 2026

• InferCNA plot logic

  navinlabcode/copykat#136 · Filter by author feiler98 opened on Jan 16, 2026

• Error : object 'anno.mat' not found

  navinlabcode/copykat#135 · Filter by author Akos-Bio-Data opened on Dec 2, 2025
  1

• CNA prediction clashing with cell type annotation

  navinlabcode/copykat#134 · Filter by author Aditya-Gautam20 opened on Nov 26, 2025

• Tumor specific Sublonal Grouping

  navinlabcode/copykat#133 · Filter by author NeuralBind opened on Oct 28, 2025

• Unupdated Code

  navinlabcode/copykat#132 · Filter by author mckoch234 opened on Oct 10, 2025

• Not.defined classification in predictions but not in matrix

  navinlabcode/copykat#131 · Filter by author ConDem94 opened on Aug 27, 2025

• Run Time

  navinlabcode/copykat#130 · Filter by author mckoch234 opened on Jun 10, 2025

• Regarding copykat, it defines aneuploidy for the specified normal group

  navinlabcode/copykat#129 · Filter by author mosy550 opened on May 23, 2025
  1

• The definition of "not.defined" in the copykat result

  navinlabcode/copykat#128 · Filter by author suanzaoren opened on May 9, 2025
  2

• Assigning discrete copy number states

  navinlabcode/copykat#127 · Filter by author melaniebalaz opened on Mar 27, 2025

• Would prediction result change if the data was splitted into multiple smaller sets?

  navinlabcode/copykat#126 · Filter by author QuinceyLv opened on Mar 10, 2025

• Help with identifying true CNVs from false

  navinlabcode/copykat#125 · Filter by author SirKuikka opened on Mar 6, 2025

• all cells are filtered

  navinlabcode/copykat#124 · Filter by author Duiduipeng opened on Jan 5, 2025
  2

• Inconsistencies in cell numbers

  navinlabcode/copykat#122 · Filter by author yitengfei120011 opened on Nov 5, 2024

• Option for users to set the seed

  navinlabcode/copykat#121 · Filter by author sjspielman opened on Oct 9, 2024

• Error in hclust(d, method = "ward.D2"): size cannot be NA nor exceed 65536

  navinlabcode/copykat#120 · Filter by author ChenlingTangMDA opened on Aug 28, 2024
  2

• Include all genes in copykat_CNA_raw_results_gene_by_cell.txt.

  navinlabcode/copykat#119 · Filter by author Prakrithi-P opened on Aug 14, 2024

• New human reference T2T CHM13

  navinlabcode/copykat#118 · Filter by author ywzhang071394 opened on Jul 31, 2024

• How to change min.gene.per.cell

  navinlabcode/copykat#117 · Filter by author rayanelkholdi opened on Jul 22, 2024
  1

• Output files are written to working directory

  navinlabcode/copykat#116 · Filter by author rVMLql58 opened on May 2, 2024
  3

• Does it make sense to run copykat on tumor samples containing very low number of normal epithelial cells?

  navinlabcode/copykat#115 · Filter by author kaizen89 opened on Apr 26, 2024
  1