User: willem.ligtenberg

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Netherlands
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https://www.wligtenber...
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wligtenberg
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2 years, 4 months ago
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Posts by willem.ligtenberg

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Misleading information in reactome.db
... Ah, yes, this was what I was afraid of. (I didn't have time to check it myself yesterday. I switched from using a Perl script that did the mapping of genes to reaction/pathways, to the mappings provided on their website. My first hunch would be that they limit their mappings to human genes, and I d ...
written 26 days ago by willem.ligtenberg110
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Comment: C: Misleading information in reactome.db
... Thank you for the feedback, I will look into those issues. ...
written 26 days ago by willem.ligtenberg110
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Comment: C: Misleading information in reactome.db
... Hi, can you please try the following package and see if it works? https://owncloud.wligtenberg.nl/index.php/s/zxb0t7hq2wt6BzM ...
written 27 days ago by willem.ligtenberg110
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Answer: A: Misleading information in reactome.db
... As the maintainer of reactome.db, I am sorry for the inconsistencies. Currently, the reactome.db package is generated using a Perl script to retrieve information from a locally installed reactome database. As previously, Reactome did not provide all the mappings we required. However, it seems that t ...
written 4 weeks ago by willem.ligtenberg110
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Answer: A: Unable to see reactome.db dbschema
... I think you have actually answered your own question. And actually found a bug. :) To get the current schema you are probably better off using sqlite (and then the .schema command) directly on the sqlite file. A while ago the schema was changed, and apparently, I did not update it in the package. ...
written 7 weeks ago by willem.ligtenberg110
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Comment: C: Reactome pathways in ReactomeDB/graphite
... Thank you for bringing this up. I also checked the reactome.db package and it also does not list the same gene ids as in the NCBI2Reactome.txt file. Interestingly, I have worked with people from Reactome to get the query correct. (could be that the query does something similar as mentioned below) I ...
written 10 weeks ago by willem.ligtenberg110
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Comment: C: Selecting few ids from reactome.db
... I understand what you mean here, but just to clarify, neither mget, nor the select function is defined in an annotation package. This behaviour comes from AnnotationDbi::select and from BiocGenerics::mget. ...
written 3 months ago by willem.ligtenberg110
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Answer: A: Selecting few ids from reactome.db
... I would say this is indeed expected behaviour. A couple of the gene ids that you list there have apparently no pathway associated with them. (At least not that ends up in any of my queries that I use to generate this package) If that in itself is an error, could you please show me, where you have ...
written 3 months ago by willem.ligtenberg110
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Comment: C: Reactome pathway names from IDs?
... yes it does. :) ...
written 16 months ago by willem.ligtenberg110
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Comment: C: Reactome pathway names from IDs?
... sure, and done! :) ...
written 16 months ago by willem.ligtenberg110

Latest awards to willem.ligtenberg

Scholar 11 months ago, created an answer that has been accepted. For A: reactome.db: reactome IDs not mapped to pathway names
Scholar 23 months ago, created an answer that has been accepted. For A: reactome.db: reactome IDs not mapped to pathway names

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