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kundajelab / coessentiality

Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)
MIT License
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Cluster membership? #4

Open bwang1324 opened 2 years ago

bwang1324 commented 2 years ago

Hello, Thank you for your paper and scripts. I am wondering if your scripts output clustering information in reference to the final 2D layout. Ie in your github there is a "clusterOne_clusters.tsv" for the sample dataset but how would I obtain a similar file if I input a different dataset? Thank you.

Wainberg commented 2 years ago

Thanks for your interest @bwang1324! You can run gene_pairs.py to generate the GLS p-values for each pair of genes, and then modules.py to run the clustering on these p-values with ClusterONE. I think @b-akshay was planning to harmonize the output of modules.py (modules_d_0.2.csv, modules_d_0.5.csv and modules_d_0.9.csv) with the input of generate_layout.py (clusterOne_clusters.tsv), but for now you may have to reformat it manually.

bwang1324 commented 2 years ago

Thank you for your response. Could you please clarify or provide sample code as to how "to harmonize the output of modules.py (modules_d_0.2.csv, modules_d_0.5.csv and modules_d_0.9.csv) with the input of generate_layout.py".

Wainberg commented 2 years ago

Thank you for your response. Could you please clarify or provide sample code as to how "to harmonize the output of modules.py (modules_d_0.2.csv, modules_d_0.5.csv and modules_d_0.9.csv) with the input of generate_layout.py".

@b-akshay?

bcollinge commented 1 year ago

Hi @Wainberg I'm also interested in this and was wondering if you or @b-akshay could provide some more information or sample code on how to harmonize the output of modules.py (modules_d_0.2.csv, modules_d_0.5.csv and modules_d_0.9.csv) with the input of generate_layout.py.

Thank you!

Wainberg commented 1 year ago

Hi @bcollinge, thanks for your interest in our work! I have to apologize - fully integrating generate_layout.py with the rest of the codebase is something that's been on @b-akshay's to do list for a while, but I'm not sure if/when it's going to happen at this point. Sorry I don't have a more positive response for you.

bcollinge commented 1 year ago

Hi @Wainberg, thank you for your response. Would it be possible to share the code that was used to generate the clusterOne_clusters.tsv file?

Wainberg commented 1 year ago

It looks like that file was generated by Akshay based on the output of modules.py. I don't have his code for the conversion, unfortunately.