HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
active 2024-02-11 → 2026-05-24 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 834 days from 2024-02-11 to 2026-05-24. Pushes: 20 total, peak 18 in a day. Pull requests: 1 total, peak 1 in a day. Issues: 25 total, peak 6 in a day. Comments: 39 total, peak 6 in a day. Stars: 27 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 |
|---|---|---|---|---|
| joachimwolff | 29 | 20 | 1 | 8 |
| bgruening | 7 | 0 | 0 | 1 |
| Abieskawa | 4 | 0 | 0 | 3 |
| usernicai | 4 | 0 | 0 | 4 |
| YiChienLee1010 | 3 | 0 | 0 | 1 |
| LucasMcNU | 3 | 0 | 0 | 3 |
| Drosophilid | 3 | 0 | 0 | 1 |
| normal-154 | 3 | 0 | 0 | 2 |
| Naveen-Ahuja | 2 | 0 | 0 | 1 |
| HengkuanLi | 2 | 0 | 0 | 1 |
| davidecarnevali | 2 | 0 | 0 | 2 |
| lixinrong0118 | 2 | 0 | 0 | 2 |
| asadrasheed002-ux | 1 | 0 | 0 | 1 |
| JianhaiChen | 1 | 0 | 0 | 1 |
| yawjalik | 1 | 0 | 0 | 1 |
| sarahmnry | 1 | 0 | 0 | 1 |
| fatimanawmi | 1 | 0 | 0 | 0 |
| ratheraarif | 1 | 0 | 0 | 1 |
| ashbymorrison | 1 | 0 | 0 | 1 |
| zhongzheng1999 | 1 | 0 | 0 | 1 |
Recent activity
Latest issues, pull requests and releases
- Issue comment#839Patrick-McKeever2026-05-24 05:12hicMergeDomains throws IndexError: list index out of range
- Issue comment#960ZED-rookie2026-03-18 07:06FATAL ERROR ML150008291L1C001R00101473806 ML150008291L1C001R00101473960 Be sure that the sam files have the same read order If using Bowtie2 or Hisat2 add the --reorder option
- Issue comment#923JianhaiChen2025-12-02 16:46Ambiguous site handling hicBuildMatrix --restrictionSequence --danglingSequence
- Issue#952Fan-iX2025-11-14 05:50hicConvertFormat shall use `"HDF5::MCOOL"` rather than `"HDF5::Cooler"` for `mcool` hdf attribute `format`
- Issue comment#913asadrasheed002-ux2025-09-26 01:43HiCPlotmatrix
- Issue comment#949normal-1542025-09-08 10:57Does it support no enzyme cleavage site ?
- Issue comment#949joachimwolff2025-09-08 07:02Does it support no enzyme cleavage site ?
- Issue comment#949normal-1542025-09-08 03:49Does it support no enzyme cleavage site ?
- Issue#949normal-1542025-09-08 03:39Does it support no enzyme cleavage site ?
- Issue#947Drosophilid2025-07-18 07:56Issue with hicPlotMatrix, Incorrect genomic range in output plot
- Issue comment#947Drosophilid2025-07-18 07:56Issue with hicPlotMatrix, Incorrect genomic range in output plot
- Issue#947Drosophilid2025-07-18 07:22Issue with hicPlotMatrix, Incorrect genomic range in output plot
- Pull request#946joachimwolff2025-07-15 18:46
- Issue#945HengkuanLi2025-07-14 03:28Issues with using hicTransform
- Issue comment#580HengkuanLi2025-07-14 03:07Different results by hicPCA and hicTransform
- Issue#944fatimanawmi2025-07-09 03:48Unexpected change in GInteractions row-count after hicNormalize / hicCorrectMatrix, and --load_raw_values flag not giving raw counts in normalized/corrected matrix
- Issue#942marija-kra2025-06-25 15:34Tips for running on a haplotype-resolved reference genome
- Issue#941lscnsdad2025-06-21 06:15hicPCA: The A/B compartments of the X chromosome is not properly recognized
- Issue comment#940joachimwolff2025-06-19 19:26TADfind
- Issue#940mandexue2025-06-19 01:23TADfind
- Issue comment#939Abieskawa2025-06-18 10:40How to interpret the result from hicBuildMatrix
- Issue comment#939Abieskawa2025-06-17 01:53How to interpret the result from hicBuildMatrix
- Issue comment#939Abieskawa2025-06-16 00:53How to interpret the result from hicBuildMatrix
- Issue comment#939joachimwolff2025-06-13 10:51How to interpret the result from hicBuildMatrix
- Issue#939Abieskawa2025-06-13 00:26How to interpret the result from hicBuildMatrix
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 27 stars here means stars gained during the window, not the repo's star count.