Issues

• different segments on CopyNumber plot

  ccagc/QDNAseq#137 · Filter by author reyescapilla opened on May 28, 2026

• Issue with QDNAseq Segmentation Output Formatting

  ccagc/QDNAseq#134 · Filter by author jihen-lau opened on Apr 4, 2025
  1

• Very low (negative) values in readcounts, copynumbers, copynumbersnormalized dataframes

  ccagc/QDNAseq#133 · Filter by author alexvasilikop opened on Mar 31, 2025
  1

• "Warning: Recycling array of length 1 in vector-array arithmetic is deprecated"

  question
  ccagc/QDNAseq#132 · Filter by author griffinfarrow opened on Mar 20, 2025
  1

• How to get annotated plot for cnv with gene names on the amplified and deleted regions?

  ccagc/QDNAseq#131 · Filter by author ralanany opened on Feb 25, 2025

• Blacklisted regions in applyFilter function without providing a bed file

  ccagc/QDNAseq#128 · Filter by author alexvasilikop opened on Jul 8, 2024

• Genome build hg38

  ccagc/QDNAseq#127 · Filter by author henryone0910 opened on May 8, 2024

• Genome for mm39

  ccagc/QDNAseq#126 · Filter by author tashaann opened on May 8, 2024

• T2T genome support

  ccagc/QDNAseq#125 · Filter by author liuyang2006 opened on May 2, 2024

• R CMD check: Sporadic test errors; Error in diff2(x, differences = diff) : names() applied to a non-vector

  ccagc/QDNAseq#123 · Filter by author HenrikBengtsson opened on Feb 14, 2024 · Next release
  3

• Is there a way to hack QDNAseq plot methods to plot a point on the log2 ratio plots?

  ccagc/QDNAseq#122 · Filter by author zetamui opened on Feb 2, 2024
  1

• Output VCF is not valid due to symbolic allele used as reference allele

  help wanted
  ccagc/QDNAseq#121 · Filter by author vlshesketh opened on Jan 15, 2024 · Next release
  7

• Marmoset bin annotation creation challenge

  ccagc/QDNAseq#119 · Filter by author kojimak324 opened on Nov 24, 2023

• Downloading 1000 Genomes samples is inactive

  ccagc/QDNAseq#118 · Filter by author kojimak324 opened on Nov 24, 2023

• Extracting reads from bam file using binReadCounts takes too long

  question
  ccagc/QDNAseq#117 · Filter by author Urja25 opened on Sep 22, 2023
  2

• How can I merge binReadCounts results?

  ccagc/QDNAseq#116 · Filter by author JYLeeBioinfo opened on Apr 6, 2023

• exportBins to seg/vcf doesn't contain all calls

  ccagc/QDNAseq#114 · Filter by author helaersr opened on Feb 21, 2023
  3

• QDNAseq 1st time issues

  ccagc/QDNAseq#111 · Filter by author RMParkes opened on Jan 9, 2023

• Directly loading counts matrix

  question
  ccagc/QDNAseq#110 · Filter by author shashwatsahay opened on Sep 22, 2022

• Export Noise Plot data

  ccagc/QDNAseq#108 · Filter by author hannesbecher opened on Apr 7, 2022

• Export segements *and* calls to same BED file

  ccagc/QDNAseq#107 · Filter by author hannesbecher opened on Apr 7, 2022

• Error in e2[[j]]: subscript out of bounds

  CGHcall package
  ccagc/QDNAseq#105 · Filter by author RodrigoGM opened on Feb 23, 2022
  1

• Running QDNAseq on WES data

  ccagc/QDNAseq#104 · Filter by author palakpatel09 opened on Feb 20, 2022
  1

• adjust the width/height of the CNV plot

  ccagc/QDNAseq#103 · Filter by author asaki1986 opened on Feb 13, 2022

• exportBins to seg/vcf when one or zero CNV are called

  bughelp wanted
  ccagc/QDNAseq#102 · Filter by author helaersr opened on Jan 27, 2022 · Next release
  9