Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
active 2024-04-18 → 2026-07-31 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 835 days from 2024-04-18 to 2026-07-31. Pushes: 160 total, peak 12 in a day. Pull requests: 56 total, peak 5 in a day. Issues: 24 total, peak 2 in a day. Comments: 66 total, peak 3 in a day. Stars: 23 total, peak 1 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 |
|---|---|---|---|---|
| fasterius | 174 | 104 | 33 | 18 |
| cavenel | 75 | 41 | 9 | 13 |
| nf-core-bot | 31 | 12 | 14 | 5 |
| github-actions[bot] | 21 | 0 | 0 | 21 |
| pinin4fjords | 6 | 3 | 0 | 1 |
| R3myG | 4 | 0 | 0 | 3 |
| sebotic | 2 | 0 | 0 | 2 |
| grst | 2 | 0 | 0 | 2 |
| Zethson | 1 | 0 | 0 | 0 |
| aguang | 1 | 0 | 0 | 0 |
| Alan-pad | 1 | 0 | 0 | 0 |
| LucFrancisENX | 1 | 0 | 0 | 0 |
| gboscagli | 1 | 0 | 0 | 0 |
| pstorozenko | 1 | 0 | 0 | 0 |
| FloWuenne | 1 | 0 | 0 | 1 |
| Chrisdoan9 | 1 | 0 | 0 | 0 |
| vella12-osu | 1 | 0 | 0 | 0 |
Recent activity
Latest issues, pull requests and releases
- Issue#142Zethson2026-05-07 12:17Accelerate scverse/scanpy steps with rapids-singlecell
- Issue comment#132github-actions[bot]2026-01-27 14:22Strict mode
- Issue#121fasterius2026-01-23 09:58Input file name collision
- Pull request#131fasterius2026-01-23 08:17
- Issue#94fasterius2026-01-16 10:09Copying `sdata_processed.zarr` to S3 yields java.nio.file.NoSuchFileException
- Issue comment#94fasterius2026-01-16 10:09Copying `sdata_processed.zarr` to S3 yields java.nio.file.NoSuchFileException
- Issue comment#121cavenel2025-12-05 13:58Input file name collision
- Issue#119cavenel2025-12-05 13:56Update the metro map
- Issue comment#123FloWuenne2025-09-30 20:16✨ feat: Added ability to use .tar files instead of just .tar.gz files…
- Issue#116pinin4fjords2025-09-23 07:51No fastq_dir specified or no samples found in folder
- Issue comment#121cavenel2025-09-18 08:06Input file name collision
- Issue#95cavenel2025-09-18 07:59Add compatibility for Visium HD
- Issue#40cavenel2025-09-18 07:59Add MultiQC report
- Pull request#101cavenel2025-09-18 07:59
- Issue#121vella12-osu2025-09-17 21:37Input file name collision
- Issue#119fasterius2025-09-05 13:23Update the metro map
- Pull request#117fasterius2025-08-21 15:07
- Pull request#118fasterius2025-08-21 15:07
- Issue comment#116fasterius2025-08-21 15:02No fastq_dir specified or no samples found in folder
- Pull request#118fasterius2025-08-21 14:56
- Pull request#117nf-core-bot2025-07-08 11:40
- Issue#116gboscagli2025-07-01 12:01No fastq_dir specified or no samples found in folder
- Issue comment#115github-actions[bot]2025-06-18 11:00Futureproofing
- Pull request#115fasterius2025-06-18 10:59
- Issue comment#114github-actions[bot]2025-06-12 13:58Update QUARTONOTEBOOK nf-core module
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 23 stars here means stars gained during the window, not the repo's star count.