Metabolomics_Seminar_Topic_10

From the paper entitled "Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes"; the figures;

• FIGURE 1
  • A
  • B
  • C
• FIGURE 3
  • A
  • B
    • i
    • ii
    • iii
    • iv
• FIGURE 5
  • A
  • B
  • C
    • i
    • ii

This repository contains efforts to reproduce these figures from scratch. The dataset used in this study includes these resources from the paper;

• FIGURE 1 -- Table_1 Source Data 1.
• FIGURE 3 -- Table_3 Source Data 3.
• FIGURE 5 -- Table_5 Source Data 5.

Installing Manually From Source

This repository compiles under Python == 3.9.18, to install Python --> pyenv

Clone the repository

git clone https://github.com/SinaBerkGolech/Metabolomics_Seminar_Topic_10.git --recursive

Create the Python virtual environment. Install virtualenv first if needed with python3 -m pip install --user virtualenv.

cd Metabolomics_Seminar_Topic_10
virtualenv -p python3 metabolomics_seminar_env
source metabolomics_seminar_env/bin/activate
python3 -m pip install -U setuptools pip wheel
python3 -m pip install -U -r requirements.txt

[1] Gavriilidou, A., Kautsar, S.A., Zaburannyi, N. et al. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat Microbiol 7, 726–735 (2022). (https://doi.org/10.1038/s41564-022-01110-2)

[2] Allen M, Poggiali D, Whitaker K et al. Raincloud plots: a multi-platform tool for robust data visualization [version 2; peer review: 2 approved]. Wellcome Open Res 2021, 4:63 (https://doi.org/10.12688/wellcomeopenres.15191.2)