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runhic

An easy-to-use Hi-C data processing software supporting distributed computation.

https://github.com/xiaotaowang/hic_pipeline

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

4d-nucleome-network arima bioinformatics chromosome-conformation-capture cooler hi-c pairs pipeline python
Last synced: 6 months ago · JSON representation

Repository

An easy-to-use Hi-C data processing software supporting distributed computation.

Basic Info
Statistics
  • Stars: 61
  • Watchers: 5
  • Forks: 22
  • Open Issues: 6
  • Releases: 1
Topics
4d-nucleome-network arima bioinformatics chromosome-conformation-capture cooler hi-c pairs pipeline python
Created about 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.rst 

runHiC
******
.. image:: https://zenodo.org/badge/doi/10.5281/zenodo.55324.svg
   :target: http://dx.doi.org/10.5281/zenodo.55324
.. image:: https://static.pepy.tech/personalized-badge/runhic?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads
   :target: https://pepy.tech/project/runhic

runHiC is an easy-to-use command-line tool for Hi-C data processing.

Since version 0.8.6, runHiC has supported data from all kinds of 3C-based experiments,
including Hi-C, Micro-C, HiChIP/PLAC-Seq, and ChIA-PET. For experiments that do not use
restriction enzymes for DNA fragmentation, you can set the enzyme name arbitrarily for your
record. For example, for Micro-C, you can set it to *MNase*; for ChIA-PET, you can set it to
*sonication*.

Since version 0.8.5, runHiC has changed the default aligner to `chromap `_,
which is comparable to `bwa-mem `_ in alignment accuracy, but runs over 10 times faster.

Since version 0.8.1, runHiC can be used directly on `Arima HiC `_ data
by setting the enzyme name to *Arima*.

Since version 0.8.0, runHiC has changed its default data container/format from HDF5 to
`Pairs `_ and
`Cooler `_. 

Design Concepts
===============
runHiC is designed to process Hi-C data from raw sequencing reads(.sra, .fastq, .fastq.gz) to the ICE-corrected
contact matrices. It currently contains 5 subcommands:

+------------+-------------------------------------------------------------------------------------------------------------------+
| mapping    | Map raw sequencing reads to a supplied genome. Support three read aligners: chromap, bwa and minimap2.            |
+------------+-------------------------------------------------------------------------------------------------------------------+
| filtering  | Perform read-level and fragment-level noise removing                                                              |
+------------+-------------------------------------------------------------------------------------------------------------------+
| binning    | 1.Generate contact matirx; 2. Perform ICE/matrix-balancing normalization                                          |
+------------+-------------------------------------------------------------------------------------------------------------------+
| pileup     | Perform the entire processing steps from *mapping* to *binning*                                                   |
+------------+-------------------------------------------------------------------------------------------------------------------+
| quality    | Evaluate the quality of your Hi-C data                                                                            |
+------------+-------------------------------------------------------------------------------------------------------------------+

Links
=====
- `Detailed Documentation `_
    - `Installation `_
    - `Quick Start `_
    - `Data Quality `_
    - `Parallel Computation `_
- `Code Repository `_ (At GitHub, Track the package issue)
- `PyPI `_ (Download and Installation)

Usage
=====
Open a terminal, type ``runHiC -h`` or ``runHiC  -h`` for help information.

Citation
========
Xiaotao Wang. (2016). runHiC: A user-friendly Hi-C data processing software based on hiclib. Zenodo.
`10.5281/zenodo.55324 `_

Owner

  • Name: Xiaotao Wang
  • Login: XiaoTaoWang
  • Kind: user
  • Location: Shanghai
  • Company: Fudan University

My research focuses on developing computational tools to study 3D genome organization and its relationship with gene regulation.

GitHub Events

Total
  • Watch event: 6
  • Fork event: 2
Last Year
  • Watch event: 6
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 390
  • Total Committers: 5
  • Avg Commits per committer: 78.0
  • Development Distribution Score (DDS): 0.577
Past Year
  • Commits: 5
  • Committers: 1
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Xiaotao Wang w****8@g****m 165
Xiaotao Wang w****6@g****m 98
Xiaotao Wang w****8@1****m 64
Xiaotao Wang X****g 62
Yunxia Liu 3****u 1
Committer Domains (Top 20 + Academic)
163.com: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 16
  • Total pull requests: 3
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 22 days
  • Total issue authors: 15
  • Total pull request authors: 3
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • shuzhangcourage (2)
  • alobo4 (1)
  • Lattesnow (1)
  • MartinLoza (1)
  • jawmest101 (1)
  • faiza-khurshid (1)
  • ucsfpan (1)
  • oriolfornes (1)
  • zuoyi93 (1)
  • kyzhu (1)
  • faustson (1)
  • mdozmorov (1)
  • cbarcl01 (1)
  • Brahmandam-Gayatri (1)
Pull Request Authors
  • mdozmorov (1)
  • skurscheid (1)
  • YunXiaLiu (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 71 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 26
  • Total maintainers: 1
pypi.org: runhic

A easy-to-use Hi-C processing software supporting distributed computation

  • Versions: 26
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 71 Last month
Rankings
Forks count: 8.7%
Stargazers count: 9.8%
Dependent packages count: 10.0%
Average: 16.5%
Dependent repos count: 21.7%
Downloads: 32.0%
Maintainers (1)
XiaoTaoWang
Last synced: 6 months ago