'GO term analysis' error

[saisaitian]

Dear author: I'm a PhD student and I enjoyed reading your paper in Nature Communications [Mapping the perturbome network of cellular perturbations]! I'm starting up my project that will also use RNAseq to measure the effects of a large TCM small molecules and I really liked your computational approach for quantifying the morphology of your single drug perturbations . I'd rerun your pipeline for calculating the morphological space so that I can get a better sense of how it works and see if I can incorporate it into my work, but unfortunately the ipynb file 3_Drug_Properties.ipynb GO Annotations part that I can't run it well. Would it be possible to help me fix? I'd really appreciate it! In addition, the raw data of [Offsides.tsv], [SIDER.tsv] and [TwoSides.tsv], could you share it with me? Looking forward to your reply！

[mcaldera]

Hi Saisaitian,glad you enjoyed the paper! Please check out the supplementary data from https://www.nature.com/articles/s41467-019-13058-9 , if I remember correctly they should contain all the necessary files! Else let me know if something is missing.Cheers, MOn 13 May 2022 16:49, saisaitian @.***> wrote:

Dear author:

I'm a PhD student and I enjoyed reading your paper in Nature Communications [Mapping the perturbome network of cellular

perturbations]! I'm starting up my project that will also use RNAseq to measure the effects of a large TCM small molecules and I really liked your computational approach for quantifying the morphology of your single drug perturbations . I'd rerun your pipeline for calculating the morphological space so that I can get a better sense of how it works and see if I can incorporate it into my work, but unfortunately the ipynb file 3_Drug_Properties.ipynb GO Annotations part that I can't run it well. Would it be possible to help me fix? I'd really appreciate it! In addition, the raw data of [Offsides.tsv], [SIDER.tsv] and [TwoSides.tsv], could you share it with me?

Looking forward to your reply！

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[saisaitian]

In fact, I run your code to get the GO data, it get errors. I carefully check your code, and I found it need to log into the database. I do not know how to fix it? In fact, I am not good at GO analysis and I want to use your code of GO in my project, but I can not run it. Could you help me to solve it? Looking forward to your reply！

[saisaitian]

Dear author: I'm a PhD student and I enjoyed reading your paper in Nature Communications [Mapping the perturbome network of cellular perturbations]! I'd rerun your pipeline for calculating the morphological space so that I can get a better sense of how it works and see if I can incorporate it into my work, but unfortunately the ipynb file 3_Drug_Properties.ipynb GO Annotations part that I can't run it well. could you share it with me? I carefully check the supplementary data . For GO analysis, it is not exist and [Offsides.tsv], [SIDER.tsv] and [TwoSides.tsv] also were lost. Hope yo get your help! Looking forward to your reply！

[mcaldera]

Hi Saisaitian,

You are right, somehow these three files were left our during our upload. Rally sorry for the inconvenience! I do think I still got the .tsv files somewhere on my old work computer (I am not anymore a PhD student in the Menche lab, so I also don’t have direct access to their resources anymore). In case not I will write Dr. Menche, as they should still have all the files on their Lab database and then sent them to you.

Cheers and asap, Michael

On 14.05.2022, at 04:53, saisaitian @.**@.>> wrote:

Dear author: I'm a PhD student and I enjoyed reading your paper in Nature Communications [Mapping the perturbome network of cellular perturbations]! I'd rerun your pipeline for calculating the morphological space so that I can get a better sense of how it works and see if I can incorporate it into my work, but unfortunately the ipynb file 3_Drug_Properties.ipynb GO Annotations part that I can't run it well. could you share it with me? I carefully check the supplementary data . For GO analysis, it is not exist and [Offsides.tsv], [SIDER.tsv] and [TwoSides.tsv] also were lost. Hope yo get your help! Looking forward to your reply！

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[saisaitian]

Thanks for your reply！ Looking forward to your sharing ! In addition, could you help me deal with the error code, so that we can use it better of GO similarity analysis? In fact, it was not work