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Hello, I am running ChemRich analysis in R using the script chemrich_chemical_classes.R. Can I use the fold change values of metabolites between two groups as the effect size? When I use fold change …
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Assuming we have a list of matched metabolites, merge 2 models via a common compartment
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In the file test-files/test_a_2a.xml with Kon/off = 0.5 at the begining some A_c are in the compartment e which shouldn't
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Hi all,
I have been experiencing a peculiar problem with my genome-scale reconstructions being unable to take up any substrates/metabolites or excrete any products/metabolites. I provide a mineral …
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Find the 'top 100' metabolites - we have a set of ~50,000 metabolites, many of which are found in multiple experiments and in multiple samples within an experiment. What are the most common metabolite…
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Hi , I am reading and running the codes of your article. But I have a question, for example, from a generic model like Human_1_17.mat, how did you make tissue-specific models like blood, kidney, hear…
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# Description of the issue
The compounds have the identical annotation but different IDs. This can then also lead to the problem of having different reaction IDs for identical reactions (examples c…
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I've experienced this error qhen i'm usting the node sygma metabolites.
Execute failed: org.knime.python2.kernel.PythonKernel.execute(Ljava/lang/String;Lorg/knime/core/node/ExecutionContext;)[Ljava…
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For the Schlosser paper, the find the ChEBI ID for the metabolites [https://app.zenhub.com/files/2995118/b4dda359-081e-437d-a978-21dafa2eabd5/download](https://app.zenhub.com/files/2995118/b4dda359-08…
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Hello, I was trying to reproduce pinocembrin production pathways by using:
- pinocembrin as the source,
- parsed (by using [RRParser](https://github.com/brsynth/RRParser)) version of reactio…