GitHub - gillislab/Family_level

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Name		Name	Last commit message	Last commit date
Latest commit History 26 Commits
Analysis_via_ortho_moved_up_to_eukaryote_level		Analysis_via_ortho_moved_up_to_eukaryote_level
Analysis_via_orthogroups		Analysis_via_orthogroups
Comparison_to_og_duplication_paper		Comparison_to_og_duplication_paper
Cross_species_framing_of_paper		Cross_species_framing_of_paper
Cross_species_module_comparison		Cross_species_module_comparison
Data_for_tutorial		Data_for_tutorial
Module_robustness		Module_robustness
Original_analysis_circa_2021		Original_analysis_circa_2021
Analysis_tutorial.ipynb		Analysis_tutorial.ipynb
LICENSE.txt		LICENSE.txt
Readme.txt		Readme.txt

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System Requirements:
Developed on Linux Rocky 9.6, but will work on any computer with the required Python Packages installed.
Tested on Linux Rocky 9.6. 
No non-standard hardware


Installation Guide:
1) Clone Repository from Github
2) Set your data directory
3) Run notebook! 

Run time: This should take <10 minutes to install and run, as tested on a home gaming PC. 

Expected output: 4.42 concordant groups/discordant for family comparisons, and 2.98 concordant genes/discordant for genewise comparisons. 

Reproduction Instructions: To repeat for all pairs of species, download and align species data from SRA, and use the files in the folder Cross_species_module_comparison/Improving_signal file. Any extra files you need will be  at https://gillisweb.cshl.edu/CoCoBLAST/ 
This should just be N-M files!