Fast, sensitive and accurate integration of single-cell data with Harmony. This fork hosts the website for harmony2
active 2023-08-17 → 2026-06-16 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 1035 days from 2023-08-17 to 2026-06-16. Pushes: 13 total, peak 2 in a day. Pull requests: 19 total, peak 3 in a day. Issues: 122 total, peak 8 in a day. Comments: 276 total, peak 13 in a day. Stars: 172 total, peak 2 in a day.
- Pushes
- Pull requests
- Issues
- Comments
- Stars
Stars, PRs, issues and forks are under-captured in the later part of this window. GH Archive progressively stopped capturing non-push events during 2026 — −95% or worse by the end of the window. Every series here except Pushes fades for that reason, so a decline above reflects the archive, not this repository. Pushes stay reliable throughout, so read them, and the contributor counts derived from them, as the real signal. Data health has the measurements.
Top contributors
Pushes, PRs, issues, reviews and comments — stars and forks excluded, so this is contribution rather than popularity
| Contributor | Contributions | Pushes | PRs | Comments |
|---|---|---|---|---|
| pati-ni | 204 | 12 | 15 | 135 |
| Yuan-9 | 12 | 0 | 0 | 10 |
| DarioS | 10 | 0 | 0 | 3 |
| ilyakorsunsky | 10 | 1 | 1 | 4 |
| anemartinezlarrinaga2898 | 8 | 0 | 0 | 8 |
| antoine4ucsd | 8 | 0 | 0 | 5 |
| ponomarevsy | 6 | 0 | 0 | 4 |
| erflynn | 6 | 0 | 0 | 4 |
| jjs847 | 6 | 0 | 0 | 6 |
| vertesy | 5 | 0 | 0 | 3 |
| jcshuy | 5 | 0 | 0 | 2 |
| DiracZhu1998 | 5 | 0 | 0 | 3 |
| qdong2023 | 5 | 0 | 0 | 1 |
| SalimMegat | 4 | 0 | 0 | 3 |
| iichelhadi | 4 | 0 | 0 | 3 |
| Carrey14 | 4 | 0 | 0 | 3 |
| YiweiNiu | 4 | 0 | 0 | 2 |
| hanst716 | 3 | 0 | 0 | 1 |
| samgest | 3 | 0 | 0 | 1 |
| jasoncrucify | 3 | 0 | 0 | 2 |
Recent activity
Latest issues, pull requests and releases
- Issue comment#291Heime-Jorgen2026-06-16 01:15K-Lean: machine-verified contracts for single-cell integration
- Pull request#282pati-ni2026-04-20 22:36
- Issue#276osschneile2026-02-10 11:56Harmony integration failed on one sample - how to fix that?
- Issue comment#135pati-ni2025-12-10 13:58Warning message for Quick-TRANSfer
- Issue comment#274pati-ni2025-11-05 15:15RunHarmony() Error on macOS: “Invalid number of ncores provided: 0. Maximum available cores: NA”
- Issue#274Krystalkeke2025-10-29 03:15RunHarmony() Error on macOS: “Invalid number of ncores provided: 0. Maximum available cores: NA”
- Issue comment#271brianlamere2025-09-15 03:01RunHarmony appears to be ignoring max_iter (and max.iter.harmony)
- Issue#273pati-ni2025-09-04 18:50merge the result from harmony
- Issue comment#271pati-ni2025-08-21 18:36RunHarmony appears to be ignoring max_iter (and max.iter.harmony)
- Issue comment#271brianlamere2025-08-21 18:14RunHarmony appears to be ignoring max_iter (and max.iter.harmony)
- Issue#271brianlamere2025-08-21 10:47RunHarmony appears to be ignoring max_iter (and max.iter.harmony)
- Issue comment#263vertesy2025-08-18 07:57Best Practices for Sequential vs. Parallel Regression of Multiple Covariates in Harmony
- Issue comment#270GoulsonWang2025-07-03 06:50Batch Correction in scRNA-seq: How to Preserve Biological Differences
- Issue comment#54jonoave2025-05-13 08:26Where are the statistics of harmony reduction stored?
- Issue comment#269doliv0712025-04-24 15:40Consider modifying `early_stop` threshold
- Issue comment#269doliv0712025-04-24 14:22Consider modifying `early_stop` threshold
- Issue comment#269pati-ni2025-04-21 14:34Consider modifying `early_stop` threshold
- Issue#270sunsunb2025-04-17 07:01Batch Correction in scRNA-seq: How to Preserve Biological Differences
- Issue comment#74LeeWang212025-04-01 07:24Can "harmony" be used in conjunction with "monocle"
- Issue comment#232Pieros123-R2025-03-26 07:55Lambda selection
- Issue#268JarneBelien2025-03-24 08:30PCA plotting of the corrected Harmony embeddings
- Issue comment#268pati-ni2025-03-22 14:00PCA plotting of the corrected Harmony embeddings
- Issue comment#268JarneBelien2025-03-22 12:21PCA plotting of the corrected Harmony embeddings
- Issue comment#268pati-ni2025-03-21 20:42PCA plotting of the corrected Harmony embeddings
- Issue#268JarneBelien2025-03-21 10:26PCA plotting of the corrected Harmony embeddings
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 172 stars here means stars gained during the window, not the repo's star count.