Manuscript: "Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction" Authors: E.S. Deutekom, T.J.P. van Dam, B. Snel https://doi.org/10.1101/2021.05.05.442724
This serves to share code and data for reproducibility.
Main analysis notebook: Improving_prediction_Sonic_final.ipynb Download data at https://doi.org/10.6084/m9.figshare.14500146 as is. Add notebook to Sonicparanoid or Broccoli folder.
Code at least needed for reproducibility, used outside of the jupyter notebook for the analyses. Previous work was done using code from: https://github.com/ESDeutekom/ComparingOrthologies/tree/master/eukarya/scripts_nonsql
- python 3.7.6
- ete3 3.1.1
- matplotlib 3.1.2
- numpy 1.18.1
- pandas 1.0.1
- scipy 1.4.1
- seaborn 0.11.1
- scikit-learn 0.22.2.
All data can be reproduced using the code provided here and previous work done in https://github.com/ESDeutekom/ComparingOrthologies/
Any data can also be sent upon request.
- BIOGRID Homo sapiens: 3.5.172.tab2.txt (https://thebiogrid.org).
- BIOGRID Saccharomyces cerevisiae S288c: 3.5.175.tab2.txt (https://thebiogrid.org).
- All pre-made files that are needed to reproduce the main results for Sonicparanoid inferred OGs in the jupyter notebook are shared with figshare (https://doi.org/10.6084/m9.figshare.14500146).
- OG files and LECA OG files:
- Sonicparanoid:
- Broccoli: