uorf4u 0.5.4

A tool for short uORF annotation.

Description

uorf4u is a bioinformatics tool for conserved upstream ORFs annotation.

Programming languages: Python3
OS: MacOS, Linux
Python dependencies: biopython, configs, argparse, pandas, statistics, logomaker, matplotlib, reportlab.
R dependencies: ggmsa, ggplot2, optparse
OS-level dependencies: mafft (v. 7.505 is included in the package)
License: WTFPL
Version: 0.5.0 (October 2022)

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/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: ..., ---, doi

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 uorf4u functionality. Please don't hesitate to share your ideas or feature requests.