Science Score: 33.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 7 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
✓Committers with academic emails
6 of 9 committers (66.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary
Repository
Software to call ROHs
Basic Info
- Host: GitHub
- Owner: hringbauer
- License: gpl-3.0
- Language: Jupyter Notebook
- Default Branch: master
- Size: 382 MB
Statistics
- Stars: 16
- Watchers: 2
- Forks: 3
- Open Issues: 2
- Releases: 1
Metadata Files
README.md
Development github repository for the software hapROH and hapCON
Harald Ringbauer, Yilei Huang, May 2022; Code released under GNU General Public License v3.0
This is the code repository intended for contributing developers (i.e. to manage code used in development and publications). The release for users is made available as an installable Python software package hapROH. The official user documentation is available at readthedocs. It contains quick-start guides as well as usage examples on test data.
There are three main parts of the hapROH package:
hapROH
Software to call ROH from ancient and present-day DNA using reference haplotypes. Author: Harald Ringbauer, September 2020 Code released under GNU General Public License v3.0
Development Code behind python package hapROH. Please refer to our online documentation for details about the current version and installation.
This is the git repository for development, as well as code used in the hapROH publication.
hapCon
hapCon is an extension of hapROH for estimaing contamination rate for male aDNA samples.
We have prepared a detailed online documentation for hapCon. In addition, a jupyter notebook guide for using our method is availble at ./Notebooks/Vignettes/hapCon_vignette.ipynb in this repository. We also have a preprint for hapCon if you are interested in more technical details and its usage limits.
hapROH with Contamination
Joint estimation of ROH blocks and Contamination Rate
Please refer to our readthedocs site for details.
Installation
You only need to install the PyPi package hapROH to use both hapCon and hapROH:
To install via pip:
pip install hapROH
To upgrade an existing installation:
pip install --upgrade hapROH
References
Scientific manuscripts introducing the methods are available at: - https://doi.org/10.1038/s41467-021-25289-w for hapROH - https://doi.org/10.1101/2021.12.20.473429 for hapCon
Owner
- Name: Harald Ringbauer
- Login: hringbauer
- Kind: user
- Location: Leipzig
- Company: Max Planck Institute for Evolutionary Anthropology
- Website: http://hringbauer.com/
- Twitter: HaraldRingbauer
- Repositories: 5
- Profile: https://github.com/hringbauer
Creating methods in computational population genetics. Focus on ancient DNA analysis. Group Leader @ Max Planck Institute, Archaeogenetics Department, Leipzig
GitHub Events
Total
- Issues event: 4
- Watch event: 2
- Issue comment event: 5
- Push event: 6
- Pull request event: 2
Last Year
- Issues event: 4
- Watch event: 2
- Issue comment event: 5
- Push event: 6
- Pull request event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| hringbauer | h****r@u****u | 256 |
| hyl317 | y****2@c****u | 143 |
| Harald Ringbauer | h****r@g****t | 139 |
| Harald Ringbauer | h****r@h****u | 26 |
| steinrue | s****e@u****u | 7 |
| Harald Ringbauer | h****r@i****t | 1 |
| Harald Ringbauer | h****r@m****l | 1 |
| Yilei Huang | h****l@Y****l | 1 |
| Ringbauer | h****7@l****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 10
- Total pull requests: 7
- Average time to close issues: about 1 month
- Average time to close pull requests: about 4 hours
- Total issue authors: 8
- Total pull request authors: 1
- Average comments per issue: 2.5
- Average comments per pull request: 0.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 1
- Average time to close issues: about 1 month
- Average time to close pull requests: 1 minute
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 1.67
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ryhui (2)
- eshab5 (2)
- pur80a (1)
- mariamnawaz1 (1)
- ngaens (1)
- TCLamnidis (1)
- jkimsis (1)
- batelz (1)
Pull Request Authors
- hringbauer (8)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 68 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 27
- Total maintainers: 1
pypi.org: haproh
Identify runs of homozygosity (hapROH) and contamination (hapCon) in low coverage ancient human DNA data (1240K SNPs) using modern reference panel
- Homepage: https://github.com/hringbauer/hapROH
- Documentation: https://haproh.readthedocs.io/
- License: GNU GPLv3
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Latest release: 0.64
published about 3 years ago
Rankings
Maintainers (1)
Dependencies
- sphinx *
- sphinx-autoapi *
- sphinx_rtd_theme *
- cython *
- h5py *
- matplotlib *
- numdifftools *
- numpy *
- pandas *
- psutil *
- pysam *
- scipy *