Issues

• Sequencing strategy different between sample to infer CNVs vs Reference

  kharchenkolab/numbat#252 · Filter by author PauloRVMendonca opened on Jun 14, 2026

• Dataset inquiry

  kharchenkolab/numbat#249 · Filter by author macelik opened on Apr 1, 2026
  1

• rtracklayer missing from singularity image

  kharchenkolab/numbat#248 · Filter by author lisannemout opened on Jan 29, 2026

• Numbat-multi with 10x Multiome

  kharchenkolab/numbat#245 · Filter by author LucileBZH opened on Dec 12, 2025

• Numbat assigns clone coloring in Panel.png not uniquely

  kharchenkolab/numbat#241 · Filter by author Mashuaiii opened on Oct 21, 2025
  1

• Error: object 'barcodes' not found in bulk mode

  kharchenkolab/numbat#238 · Filter by author ctho1 opened on Sep 14, 2025
  1

• Error in h(simpleError(msg, call)), consider using another log_formatter or skip_formatter on strings with curly braces?

  kharchenkolab/numbat#233 · Filter by author Gonnamu opened on Jul 1, 2025

• Allele specific copy numbers for 'amp' and calculation of cnv_state_post

  kharchenkolab/numbat#228 · Filter by author kzb193 opened on May 27, 2025
  1

• Output file with separate nMajor and nMinor columns instead of cnv_state

  kharchenkolab/numbat#226 · Filter by author ecibola opened on May 12, 2025

• Expression reference dataset giving high noise and tumor proportion

  kharchenkolab/numbat#224 · Filter by author katiedaco-diamondage opened on May 2, 2025
  1

• how to create the phasing reference panel - No X-chromosome currently

  kharchenkolab/numbat#222 · Filter by author ejscience opened on Apr 9, 2025

• Questions About Running Numbat on Two Samples

  kharchenkolab/numbat#221 · Filter by author EmanueleCalvi opened on Mar 20, 2025
  1

• no genetic map

  kharchenkolab/numbat#219 · Filter by author tanya-karagiannis opened on Mar 17, 2025

• Joint probability calculations

  kharchenkolab/numbat#217 · Filter by author idkaavan opened on Mar 3, 2025
  1

• Request: expression only samples

  kharchenkolab/numbat#216 · Filter by author Thapeachydude opened on Jan 29, 2025

• Running pileup_and_phase.R on Parse bam files

  kharchenkolab/numbat#213 · Filter by author Zgautier opened on Dec 17, 2024

• monoallelic vs ballelic deletions

  kharchenkolab/numbat#212 · Filter by author nbahlis opened on Nov 8, 2024

• Analysis for the X chromosomes.

  kharchenkolab/numbat#211 · Filter by author gsato3105 opened on Nov 4, 2024
  1

• Refining tumor/normal assignment

  kharchenkolab/numbat#209 · Filter by author nandobonf opened on Oct 29, 2024
  5

• How to handle bulk_clones_final CNV states when segs_consensus_fix is provided

  kharchenkolab/numbat#208 · Filter by author teng-gao opened on Oct 22, 2024

• Numbat running for two samples separately but crashes when I merge the two and perform the same analysis again

  kharchenkolab/numbat#203 · Filter by author quail768 opened on Aug 26, 2024
  5

• Better error handling?!

  kharchenkolab/numbat#202 · Filter by author stela2502 opened on Aug 13, 2024

• (hom_rate > 0.4) {: missing value where TRUE/FALSE needed

  tofix
  kharchenkolab/numbat#200 · Filter by author stela2502 opened on Aug 6, 2024
  3

  

• Error in vectbl_assign(x[[j]], i, recycled_value[[j]]): DLL requires the use of native symbols

  kharchenkolab/numbat#197 · Filter by author stela2502 opened on Jul 19, 2024
  6

• CNV calling from 10X 5 prime GEX data

  kharchenkolab/numbat#193 · Filter by author cv55 opened on Jun 14, 2024
  4