A tool for short uORF annotation.
Project description
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.
OS-level dependencies: mafft (v7.490 is included in the package)
License: WTFPL
Version: 0.6.4 (October 2022)
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/art-egorov/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, bioRxiv 2022.10.27.514069; doi: 10.1101/2022.10.27.514069
Contact
Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.
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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.