HMMRATAC peak caller for ATAC-seq data
active 2023-08-22 → 2025-01-02 (UTC)
Complete coverage26,344 / 26,344 hourly files (100%) · 2 absent upstream2023-08-15 → 2026-08-16 (UTC)
Events
32
Pushes
5
Pull requests
0
Issues
6
Stars
11
Forks
3
Activity over time
Daily event counts in the loaded window
Line chart, 500 days from 2023-08-22 to 2025-01-02. Pushes: 5 total, peak 5 in a day. Pull requests: 0 total, peak 0 in a day. Issues: 6 total, peak 1 in a day. Comments: 7 total, peak 2 in a day. Stars: 11 total, peak 1 in a day.
- Pushes
- Pull requests
- Issues
- Comments
- Stars
Top contributors
Pushes, PRs, issues, reviews and comments — stars and forks excluded, so this is contribution rather than popularity
| Contributor | Contributions | Pushes | PRs | Comments |
|---|---|---|---|---|
| EvanTarbell | 5 | 5 | 0 | 0 |
| lillianj97 | 2 | 0 | 0 | 0 |
| SergioRodLla | 2 | 0 | 0 | 2 |
| chklee30 | 1 | 0 | 0 | 1 |
| wcalicow | 1 | 0 | 0 | 1 |
| wzcc-hub | 1 | 0 | 0 | 1 |
| olechnwin | 1 | 0 | 0 | 0 |
| dulcirena | 1 | 0 | 0 | 0 |
| simontimmins | 1 | 0 | 0 | 1 |
| ijeomameremikwu | 1 | 0 | 0 | 0 |
| hrayjones | 1 | 0 | 0 | 1 |
| eggrandio | 1 | 0 | 0 | 0 |
Recent activity
Latest issues, pull requests and releases
- Issue#109eggrandio2024-10-24 16:39Q: Using peak summits for footprinting/TF binding motif analysis ? Do they need to be shifted ?
- Issue comment#108wcalicow2024-10-24 06:19Q: How is the fourth column calculated for the digested_short.bdg, digested_mono.bdg, digested_di.bdg, and digested_tri.bdg output files when using the the flag --digested.
- Issue comment#49chklee302024-10-09 21:35BR: HMMRATAC fails due to SAM validation error?
- Issue comment#49simontimmins2024-06-14 13:26BR: HMMRATAC fails due to SAM validation error?
- Issue#108ijeomameremikwu2024-05-29 16:47Q: How is the fourth column calculated for the digested_short.bdg, digested_mono.bdg, digested_di.bdg, and digested_tri.bdg output files when using the the flag --digested.
- Issue comment#101hrayjones2024-03-25 16:58Q: Gold standard files to benchmark peak callers
- Issue#107dulcirena2024-02-09 12:55Q: I am working with a small genome (34 Mb) and I would like to ask for your advice on how to tune the default parameters. For instance, I thought it would make sense to change the window size (--window) and the maximum number of training regions to use during model building (--maxTrain). Thanks!
- Issue comment#85SergioRodLla2024-01-16 12:35Q: Peaks are too long and peak number is low
- Issue comment#102SergioRodLla2024-01-16 10:41Why the 4th column of bedgraph file values are E0, E1 and E2? What is the meaning of these values?
- Issue comment#49wzcc-hub2023-09-11 08:05BR: HMMRATAC fails due to SAM validation error?
- Issue#106lillianj972023-09-08 05:19BR:
- Issue#106lillianj972023-09-07 10:37BR:
- Issue#105olechnwin2023-08-22 21:37Q: gappedPeak file visualization in IGV and interpretation
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 11 stars here means stars gained during the window, not the repo's star count.