AntonioDeFalco/SCEVAN

Issues

• No tumor cell found in output but tumor cell reported in log

  #125 opened a month ago by chenhong-dkfz
  0

• Allow precomputed baseline for single sample pipeline

  #124 opened 2 months ago by wudustan
  4

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

  #119 opened 4 months ago by royfrancis
  2

• Results from a Normal sample gives all tumor predictions

  #118 opened 2 months ago by Prakrithi-P
  1

• Correlation number of genes/counts

  #123 opened 2 months ago by Ilarius
  1

• Error: address 0x210c0, cause 'memory not mapped'

  #120 opened 4 months ago by ywzhang071394
  2

• Genes NOT in order of chromosomal location, how big an issue?

  #122 opened 3 months ago by DGladish
  1

• class "filtered" of cells

  #121 opened 3 months ago by Ilarius
  1

• multiSampleComparisonClonalCN Error in vegaMC_R(mtx = mtx, output_file_name = paste("./output/", sample, : NA/NaN/Inf in foreign function call (arg 1)

  #117 opened 5 months ago by Prakrithi-P
  1

• Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 6435, 5148

  #115 opened 5 months ago by Ahmed-Ghobashi
  7

• Running samples together versus one by one

  #116 opened 5 months ago by kar6425
  2

• How to deal with EnsDb.Hsapiens.v86?

  #114 opened 6 months ago by autumnfe
  1

• [Error] mtx[!Dupl_GeneName, ] : (subscript) logical subscript too long

  #113 opened 6 months ago by autumnfe
  2

• error in colnames<-(*tmp*, value = colnames(geData)) : attempt to set 'colnames' on an object with less than two dimensions

  #75 opened 6 months ago by Githubxsw
  8

• About only tumor cell (cluster)

  #112 opened 6 months ago by soralsr
  1

• Issue with setting norm_cell

  #92 opened 6 months ago by LASeeker
  3

• Error in data.frame - arguments imply differing number of rows

  #109 opened 6 months ago by augjensen
  2

• Remove filtering of duplicate gene symbols when rownames of counts matrix are Ensembl IDs

  #111 opened 6 months ago by allyhawkins
  1

• Filtered cells in pre-filtered dataset

  #110 opened 7 months ago by EmanueleRosatti
  2

• control over cell/gene filtering

  #98 opened 7 months ago by andynkili
  1

• Error in `[.data.frame`(res_class$CNAmat, , res_class$tum_cells) : undefined columns selected

  #97 opened a year ago by DGladish
  1

• Question about beta_vega and normal/tumor calls

  #100 opened 7 months ago by mloberg16
  1

• Error in x$tmp_NES: $ operator is invalid for atomic vectors

  #102 opened 7 months ago by cmills2
  2

• Error in dataframe *tmp* replacement has x data has y

  #106 opened 7 months ago by sinanassiri
  1

• some clarifications

  #107 opened 8 months ago by aleednn
  2

• Max # confident normal cells when specifying norm_cell?

  #103 opened 9 months ago by DGladish
  2

• Restrictions on input files

  #99 opened 9 months ago by Mashuaiii
  2

• Error in names(segmList)

  #94 opened 9 months ago by asl58
  3

• CNA integer states on UMAP

  #90 opened 9 months ago by RaghadShu
  1

• Inconsistence of copy number profile

  #79 opened 9 months ago by wbf520qcp
  1

• Does SCEVAN have a requirement for the minimum number of cells?

  #105 opened 9 months ago by BioAmelie
  2

• How to use ENSEMBL IDs

  #104 opened 9 months ago by lorenzoamir
  1

• Is there a maximum of subclones?

  #93 opened a year ago by augjensen
  1

• Would it be possible to have a new tag/release?

  #101 opened 10 months ago by pcm32
  1

• Error in analysis of an epithelial cluster

  #96 opened a year ago by andrianamanousidaki
  0

• Compare CNV profiles across many patients

  #89 opened a year ago by augjensen
  2

• Plots

  #95 opened a year ago by DGladish
  0

• Normalization?

  #91 opened a year ago by DGladish
  2

• is there anyway to extract the percentage of sub-clones from the oncoheat data?

  #86 opened a year ago by mbihie
  1

• Copy Number with Decimals?

  #88 opened a year ago by dchavre
  0

• How to find CN for a cell (using data from heatmap)

  #87 opened a year ago by dchavre
  0

• How can I compare the copy number variation of two different types of tumour cells?

  #76 opened a year ago by mbihie
  3

• Figure format

  #78 opened a year ago by wbf520qcp
  0

• raw count matrix (tumor vs normal)

  #77 opened a year ago by mbihie
  1

• exporting the results of OncoHeat for all chromosome position

  #80 opened a year ago by moOsmanMD
  2

• Converting raw values of CNA matrix to AMP, GAIN, Normal, LOSS, DEL.

  #82 opened a year ago by moOsmanMD
  1

• is there anyway to extract the deletions from CNAmtx.RData for downstream analysis?

  #83 opened a year ago by mbihie
  1

• Raw counts in the instructions are inconsistent with examples?

  #84 opened a year ago by ahdee
  1

• What do the columns CN and segm.mean represent for the "CN.seg" file?

  #85 opened a year ago by mbihie
  1

• is there any way to run a Wilcox test (or any other statistical test) with the scevan output?

  #81 opened a year ago by mbihie
  0