a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution
active 2024-08-02 → 2026-04-21 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 628 days from 2024-08-02 to 2026-04-21. Pushes: 7 total, peak 2 in a day. Pull requests: 2 total, peak 1 in a day. Issues: 30 total, peak 3 in a day. Comments: 45 total, peak 5 in a day. Stars: 33 total, peak 3 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 |
|---|---|---|---|---|
| ForwardYang98 | 40 | 6 | 0 | 22 |
| shippp-zz | 10 | 0 | 0 | 7 |
| jairaj-mathur | 6 | 0 | 0 | 3 |
| Thapeachydude | 4 | 0 | 0 | 2 |
| zhouxw27 | 3 | 0 | 0 | 1 |
| CocoGzh | 3 | 0 | 0 | 2 |
| HarryZhang1224 | 2 | 0 | 0 | 1 |
| DontCareYaYa | 2 | 0 | 0 | 1 |
| elise-smith | 2 | 0 | 0 | 2 |
| ProDong0512 | 2 | 0 | 0 | 2 |
| lemondll | 1 | 0 | 0 | 0 |
| Li-ZhiD | 1 | 0 | 0 | 0 |
| 13acts | 1 | 0 | 1 | 0 |
| ZJUFanLab | 1 | 1 | 0 | 0 |
| jackytamkc | 1 | 0 | 1 | 0 |
| christophechu | 1 | 0 | 0 | 1 |
| yitengfei120011 | 1 | 0 | 0 | 0 |
| mbaardwijk | 1 | 0 | 0 | 0 |
| watermelontreesjs | 1 | 0 | 0 | 0 |
Recent activity
Latest issues, pull requests and releases
- Pull request#29jackytamkc2026-04-21 12:50
- Issue#27yitengfei1200112026-02-28 01:50model = sn.tr.Runner(adata=adata, device='cuda:0', verbose=False)
- Issue comment#24elise-smith2026-02-23 08:48No module named 'scniche'
- Issue comment#24elise-smith2026-02-09 18:03No module named 'scniche'
- Issue#26mbaardwijk2026-02-03 13:10Multi-slice analysis of deconvolved Visium data without ground truth regions/celltypes
- Issue comment#23ForwardYang982025-10-04 02:49Celltype granularity
- Issue#22zhouxw272025-09-29 15:52Cannot import scniche
- Issue comment#22zhouxw272025-09-29 15:52Cannot import scniche
- Issue#22zhouxw272025-09-29 15:09Cannot import scniche
- Issue comment#9Thapeachydude2025-09-19 10:57Recommendations for multi-modal, multi-slice spatial data
- Issue comment#21ForwardYang982025-09-10 08:57batch_num
- Issue comment#19Thapeachydude2025-09-04 22:31ValueError: Expected n_neighbors <= n_samples_fit, but n_neighbors = 21, n_samples_fit = 10, n_samples = 10
- Issue#19Thapeachydude2025-09-04 22:31ValueError: Expected n_neighbors <= n_samples_fit, but n_neighbors = 21, n_samples_fit = 10, n_samples = 10
- Issue comment#19ForwardYang982025-09-04 02:16ValueError: Expected n_neighbors <= n_samples_fit, but n_neighbors = 21, n_samples_fit = 10, n_samples = 10
- Issue comment#16ProDong05122025-08-30 15:52Is it compatible with silicon chip
- Issue comment#9ForwardYang982025-08-29 01:37Recommendations for multi-modal, multi-slice spatial data
- Issue#18ForwardYang982025-08-29 01:25Remove batch effect and Deconvolution
- ReleaseForwardYang982025-08-11 02:23scNiche v1.1.1
- Issue#2ForwardYang982025-08-09 00:33Function parameter description
- Issue#14ForwardYang982025-08-09 00:33Is it algorithmically valid to perform two rounds of Niche identification with ScNiche?
- Issue#13ForwardYang982025-08-09 00:32How to process multiple 50 slices of 10x Visium data without deconvolution
- Pull request#1713acts2025-08-04 05:14
- Issue comment#15ForwardYang982025-05-16 03:44Slight inconsistency in results despite identical data, code, and hardware
- Issue#15shippp-zz2025-05-16 02:34Slight inconsistency in results despite identical data, code, and hardware
- Issue comment#14ForwardYang982025-05-14 10:58Is it algorithmically valid to perform two rounds of Niche identification with ScNiche?
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 33 stars here means stars gained during the window, not the repo's star count.