icbi-lab/infercnvpy

Issues

• Alternative way to get genomic positions

  #144 opened 2 months ago by grst
  2

• gtfparse dependency causes issues with latest numpy, pandas and pyarrow

  #143 opened 2 months ago by zktuong
  2

• gene location and CNV calculation windows

  #142 opened 2 months ago by bioorange
  2

• Can the infercnvpy output observation.txt file like inferCNV(R)?

  #141 opened 2 months ago by XinheG
  2

• Encountering an ImportError with conda environment

  #139 opened 2 months ago by Richard-D-Watson
  1

• Per gene copy number signal.

  #128 opened 5 months ago by sohrabsa
  5

• ValueError: Reference must match the number of genes in AnnData.

  #134 opened 5 months ago by HZT55
  3

• stable release

  #121 opened a year ago by wangjiawen2013
  3

• Are we able to use output of infercnvpy for drawing phylogenetic trees?

  #88 opened 8 months ago by tingxie2020
  1

• Using reference datasets

  #33 opened 8 months ago by dariarom94
  1

• Adding copykat cell.line parameter?

  #123 opened 10 months ago by josephreplogle
  2

• infercnvpy.tl.infercnv result matrix is of incorrect dimensionality

  #122 opened 10 months ago by sean-at-tessera
  2

• Accessing Metadata from AnnData

  #50 opened 2 years ago by shahrozeabbas
  6

• genomic_position_from_gtf Attribute Error

  #108 opened a year ago by Tester3454
  3

• TypeError: read_csv() got an unexpected keyword argument 'sep' in infercnvpy.io.genomic_position_from_gtf

  #86 opened a year ago by huai-su
  7

• rename toggle_string_cache to enable_string_cache

  #107 opened a year ago by christophechu
  3

• Limit color scale heat map

  #63 opened a year ago by ccruizm
  3

• infercnvpy.pl.chromosome_heatmap doesn't pass dendrogram data to scanpy.pl.heatmap

  #109 opened a year ago by jpintar
  3

• NA/NaN/Inf in foreign function call (arg 10)

  #49 opened a year ago by lacey359
  1

• copykat py2rpy error

  #40 opened a year ago by diyang1354
  2

• Identifying spike-in cells using InferCNVpy

  #14 opened a year ago by mibo1996
  4

• cnv.tl.infercnv error

  #69 opened a year ago by Dacy34
  3

• The tutorial may need to be updated

  #45 opened a year ago by simon7073
  0

• copykat with mouse data

  #91 opened 2 years ago by muntajihad
  8

• need at least one array to concatenate when doing cnv.tl.infercnv()

  #27 opened 3 years ago by hyjforesight
  12

• Citation

  #34 opened 3 years ago by FlorianBarkmann
  4

• infercnvpy.pl.chromosome_heatmap shows 1e9 map values for copykat results

  #78 opened 2 years ago by zsfrbkv
  4

• inferCNV output matrix has the same dimension with different window size

  #74 opened 2 years ago by YubinXie
  2

• Inconsistent use_rep usage through src files

  #76 opened 2 years ago by zvittorio
  2

• copycat memory issue

  #75 opened 2 years ago by YubinXie
  2

• how are gene counts in groups that are all 0 handled

  #73 opened 2 years ago by amjass12
  0

• heatmap function is not recognising dendogram

  #71 opened 2 years ago by mmfalco
  2

• genomic_position_from_gtf

  #65 opened 2 years ago by Hafsa-Faeth
  2

• Shape of the output of cnv.tl.infercnv

  #37 opened 2 years ago by FlorianBarkmann
  1

• How to adjust the scale bar of chromosome_heatmap

  #38 opened 2 years ago by hyjforesight
  6

• Ith score

  #41 opened 2 years ago by rahhhm
  4

• CopyKAT - got an unexpected keyword argument 'norm_cell_names'

  #39 opened 3 years ago by sandrav-CGEN
  2

• Make nextflow pipeline to run copyKAT and SCEVAN

  #28 opened 3 years ago by grst
  2

• Add a tool for ITHCNA

  #29 opened 3 years ago by grst
  2

• add SCEVAN

  #26 opened 3 years ago by grst
  1

• Add copykat to tutorial

  #23 opened 3 years ago by grst
  5

• Add to Bioconda

  #22 opened 3 years ago by grst
  1

• Pre-processing data?

  #13 opened 3 years ago by mibo1996
  2

• summary bug

  #17 opened 3 years ago by abyssum
  2

• Heatmap chrom lenght - col width

  #18 opened 3 years ago by abyssum
  1

• considering numerically order the chromosome label `chr_pos` on the `chromosome_heatmap` function?

  #15 opened 3 years ago by jingxinfu
  9

• provided out is the wrong size for the reduction

  #12 opened 3 years ago by chsher
  1

• ValueError: need at least one array to concatenate

  #7 opened 4 years ago by mibo1996
  11

• Function to classify malignant/non-malignant cells

  #11 opened 4 years ago by rgranit
  2

• What are the units of 'window_size'?

  #8 opened 4 years ago by rgranit
  2