Description
uORF4u is a bioinformatics tool for conserved upstream ORF annotation.
Programming language: Python3
OS: MacOS, Linux
Python dependencies: biopython, configs, argparse, pandas, statistics, logomaker, matplotlib, reportlab.
Python version: >= 3.7
OS-level dependencies: mafft (v7.490 is included in the package)
License: CC0
Version: 0.9.7 (September 2025)
Web version is available at the Atkinson Lab Server Portal: server.atkinson-lab.com/uorf4u
Detailed documentation
Installation 🛠️
- The most stable release of uorf4u can be installed directly from pypi:
python3 -m pip install uorf4u
- The development version is available at github :
git clone https://github.com/GCA-VH-lab/uorf4u.git
cd uorf4u
python3 -m pip install --upgrade pip
python3 -m pip install wheel
python3 setup.py sdist bdist_wheel
python3 -m pip install -e .
! If you're a linux user, run uorf4u --linux post-install command once to update paths in the premade config files that set by default for MacOS users.
Reference 📃
If you find uorf4u useful, please cite:
Artyom. A. Egorov, Gemma C. Atkinson, uORF4u: a tool for annotation of conserved upstream open reading frames, Bioinformatics, Volume 39, Issue 5, May 2023, btad323; doi: 10.1093/bioinformatics/btad323
Contact 📇
Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.
You can also use Discussions section for sharing your ideas or feature requests!
Authors 👨🏻💻
uORF4u is developed by Artyom Egorov at the Atkinson Lab, Department of Experimental Medical Science, Lund University, Sweden 🇸🇪. We are open for suggestions to extend and improve svist4get functionality. Please don't hesitate to share your ideas or feature requests.
1 maintainer
Metadata
1 maintainer
Release files for uorf4u 0.9.7
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| uorf4u-0.9.7.tar.gz | 38.3 MB | Without provenance | Details for uorf4u-0.9.7.tar.gz |
Release files / uorf4u-0.9.7.tar.gz
| Download URL | uorf4u-0.9.7.tar.gz |
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| Size | 38.3 MB |
| Tags | Source |
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