Installation

To use MEANtools, prepare the meantools repository:

1conda create -n meantools
2conda activate meantools
3export SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True
4export LC_ALL=en_US.UTF-8
5export LANG=en_US.UTF-8
6git clone https://github.com/kumarsaurabh20/meantools.git
7cd meantools
8conda env update -f environment.yml

Warning

MEANtools is tested on Python=3.8.13 and Pandas=1.4.3. From Pandas version >=2.0.0, the support for append function has been deprecated for dataframes. We will fix the dependency issues in the upcoming version.

Note

Download additional files from https://zenodo.org/records/15697913 and move them into the directory where you cloned meantools. Additional files include:

  1. SQLite formatted LOTUS database

  2. RetroRules cross-referenced data. Mentioned in the paper as loose, medium, and strict dataset.

  3. EC-PFAM mapping file.

  4. RNA-seq normalised gene expression matrix from Jeon et al. (2020).