navinlabcode/copykat

Issues

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

  #120 opened a month ago by ChenlingTangMDA
  0

• Include all genes in copykat_CNA_raw_results_gene_by_cell.txt.

  #119 opened 2 months ago by Prakrithi-P
  0

• New human reference T2T CHM13

  #118 opened 2 months ago by ywzhang071394
  0

• How to change min.gene.per.cell

  #117 opened 2 months ago by Rayan21100
  0

• Output files are written to working directory

  #116 opened 5 months ago by rVMLql58
  3

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

  #115 opened 5 months ago by kaizen89
  1

• macrophages with CNV?

  #107 opened 10 months ago by sadiexiaoyu
  1

• Error in norm.mat.relat[which(DR2 >= UP.DR), ] : subscript out of bounds

  #88 opened a year ago by GQLL
  1

• The results of diploid and aneuploid are reversed in test_copykat_heatmap.jpeg, why?

  #99 opened a year ago by lj20220425
  5

• Heatmap cannot be plotted

  #95 opened a year ago by Yijia-Jiang
  3

• Could Copycat be used for zebrafish analysis?

  #105 opened a year ago by UEATTOOMUCH260
  1

• Outputs Heatmap Copykat

  #114 opened 6 months ago by LeaLe88
  0

• Error in .External2(C_X11, paste0("jpeg::", quality, ":", filename), g$width

  #103 opened a year ago by decodebiology
  3

• Error in step 2: arguments imply differing number of rows

  #112 opened 7 months ago by carbui
  0

• Diploid and aneuploid reversed

  #111 opened 7 months ago by LeaLe88
  0

• Error in hclust(parallelDist::parDist(t(tumor.mat), threads = 4, method = "euclidean"), : must have n >= 2 objects to cluster

  #110 opened 7 months ago by LeaLe88
  1

• Example breast tumours Error in Step 4 - heatmap

  #109 opened 7 months ago by LeaLe88
  0

• Tumor subclone

  #108 opened 8 months ago by Mashuaiii
  0

• how to translate the copykat results to inferCNV i6 HMM (the six-state CNV model)

  #106 opened 10 months ago by sadiexiaoyu
  0

• running at lower resolution

  #104 opened a year ago by vravik
  0

• WARNING! NOT CONVERGENT!

  #98 opened a year ago by stroke1989
  4

• Error in cluster mode

  #83 opened 2 years ago by AClab-sgarcia
  1

• WARNING! NOT CONVERGENT! number of iterations= 500

  #102 opened a year ago by mbihie
  1

• Adding gene annotation to CNAmatrix + p and q information

  #101 opened a year ago by RaghadShu
  1

• Question regarding "GMM definition mode"

  #100 opened a year ago by sjspielman
  0

• Error in step4

  #97 opened a year ago by 13021969200
  0

• Too many cells and the heatmap too big too open!

  #80 opened 2 years ago by liaoshengguang
  1

• Error in step 5 when trying copykat for Visium Spatial Transcriptomics data

  #96 opened a year ago by linhuawang
  0

• CNV filtering

  #94 opened a year ago by SirKuikka
  0

• Suggestions on running copykat for multiple samples without cell type annotation?

  #93 opened a year ago by Yijia-Jiang
  0

• The error 'mcfork(): Unable to fork: Cannot allocate memory' when I run copykat

  #92 opened a year ago by caodudu
  1

• CNAmat does not contain gene symbol when using genome = "hg20"

  #90 opened a year ago by WT215
  1

• "step 4: measuring baselines ...": Error in mixtools::normalmixEM(data.c, lambda = rep(1, 3)/3, mu = c(-0.2, : NA/NaN/Inf in foreign function call (arg 4)

  #91 opened a year ago by confiya
  0

• Is there any way to make re-analysis easier when change the parameter KS.cut?

  #89 opened a year ago by yunbokai
  0

• what reason of copykat analysis one sample compare to different samples with different result

  #87 opened a year ago by zqmiao-mzq
  0

• Whole genome duplication

  #86 opened a year ago by Leticia314
  0

• Question - usage for bulk RNAseq

  #85 opened a year ago by akaviaLab
  0

• copykat issue: error in step 4

  #84 opened 2 years ago by YubinXie
  2

• step 4 error

  #81 opened 2 years ago by fpengstudy
  1

• Question about define subpopulations of aneuploid tumor cells

  #82 opened 2 years ago by lwlive
  0

• Normal cells assigned as aneuploid

  #79 opened 2 years ago by AnnaAntonatouPap
  0

• Runing multiple times using same data but generate different results

  #76 opened 2 years ago by MaHaoran627
  1

• Error in match.arg(type) : 'arg' must be of length 1

  #78 opened 2 years ago by Lukadon77
  0

• Can CopyKAT be used to distinguish normal cells from tumor cells in hematological tumors？

  #77 opened 2 years ago by HengqiLiu
  0

• Issue about dlm

  #73 opened 2 years ago by Junedays
  2

• no applicable method for 'dlmSmooth' applied to an object of class "c('double', 'numeric')"

  #71 opened 2 years ago by 050114dragon
  6

• Installation failure

  #75 opened 2 years ago by SGIlabes
  0

• Error in hclust(d, method = "ward.D2") :

  #74 opened 2 years ago by qiangfan2022
  0

• Segmentation by chromosome arm size

  #72 opened 2 years ago by jgarces02
  0

• MHC genes and cell cycle genes are not filtered out in mouse version

  #70 opened 2 years ago by sky1ove
  0