Issues

• Clarify the stabilized diversity objective and frozen-count update

  bug
  immunogenomics/harmony#294 · Filter by author fderop opened on Aug 31, 2026
  2

• Hello, I am conducting scATAC-seq analysis using the software ArchR. When executing addHarmony, an error occurs, indicating that the object 'HarmonyMatrix' cannot be found.

  response needed
  immunogenomics/harmony#289 · Filter by author wujian-njau opened on May 30, 2026
  3

• Harmony v2.0.3 Fails to Integrate Data Effectively Compared to v1.2.4

  immunogenomics/harmony#288 · Filter by author xiao00su opened on May 26, 2026
  3

• Harmony integration failed on one sample - how to fix that?

  immunogenomics/harmony#276 · Filter by author osschneile opened on Feb 10, 2026
  3

• RunHarmony() Error on macOS: “Invalid number of ncores provided: 0. Maximum available cores: NA”

  response needed
  immunogenomics/harmony#274 · Filter by author Krystalkeke opened on Oct 29, 2025
  3

• Sporadic test failure on Windows

  immunogenomics/harmony#272 · Filter by author mfansler opened on Aug 22, 2025

• RunHarmony appears to be ignoring max_iter (and max.iter.harmony)

  immunogenomics/harmony#271 · Filter by author brianlamere opened on Aug 21, 2025
  4

• Batch Correction in scRNA-seq: How to Preserve Biological Differences

  immunogenomics/harmony#270 · Filter by author sunsunb opened on Apr 17, 2025
  1

• Consider modifying early_stop threshold

  immunogenomics/harmony#269 · Filter by author doliv071 opened on Apr 14, 2025
  5

• Clustering by variable and not by UMAP after RunHarmony

  immunogenomics/harmony#266 · Filter by author RRingquist opened on Jan 27, 2025
  1

• Changes in 1.2.3

  immunogenomics/harmony#265 · Filter by author wudustan opened on Dec 3, 2024
  1

• Typo in detailed walkthrough?

  immunogenomics/harmony#264 · Filter by author dariober opened on Nov 9, 2024

• Best Practices for Sequential vs. Parallel Regression of Multiple Covariates in Harmony

  immunogenomics/harmony#263 · Filter by author vertesy opened on Nov 5, 2024
  3

• Is Regressing Covariates in Both ScaleData and RunHarmony Redundant and Potentially Problematic?

  immunogenomics/harmony#262 · Filter by author vertesy opened on Nov 5, 2024

• different clustering results

  question
  immunogenomics/harmony#259 · Filter by author HarteNuss opened on Sep 10, 2024
  1

• integrating snRNA (from multiome dataset) with scRNA public dataset

  question
  immunogenomics/harmony#258 · Filter by author Urja25 opened on Sep 5, 2024
  1

• The error of harmony after subsetting data

  question
  immunogenomics/harmony#256 · Filter by author Carrey14 opened on Aug 21, 2024
  2

• how to use harmony for Seurat Spatial Data?

  immunogenomics/harmony#254 · Filter by author flpxn7 opened on Jul 24, 2024
  1

• advice about parameters for integration

  immunogenomics/harmony#251 · Filter by author javiers1983 opened on May 24, 2024

• "Is It Feasible to Use Harmony Directly for Batch Correction in Seurat V5 Instead of “ IntegrateLayers“?"

  immunogenomics/harmony#249 · Filter by author Tylesteven opened on Apr 20, 2024
  5

• Can i obtain my original data shape?

  immunogenomics/harmony#247 · Filter by author leeleavitt opened on Mar 6, 2024
  4

• Cannot reproduce Seurat.ipynb vignette; parameters not passed

  response needed
  immunogenomics/harmony#243 · Filter by author Nichal123 opened on Feb 19, 2024
  4

• vars_use Definition Not Explicit

  immunogenomics/harmony#242 · Filter by author DarioS opened on Feb 19, 2024

• Convergence plot showing bizarre reading, data okay to use?

  immunogenomics/harmony#241 · Filter by author jcshuy opened on Feb 14, 2024
  2

• Plotting Function do_scatter Does Not Exist

  immunogenomics/harmony#239 · Filter by author DarioS opened on Feb 2, 2024
  1