User: willem.ligtenberg

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wligtenberg
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Posts by willem.ligtenberg

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Change in pathway IDs scheme in reactome.db
... I didn't update the version number (maybe should have...)   ...
written 10 hours ago by willem.ligtenberg120
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Comment: C: Change in pathway IDs scheme in reactome.db
... mmm, version 60 of Reactome was released, should I run a quick update? ...
written 3 days ago by willem.ligtenberg120
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Comment: C: Change in pathway IDs scheme in reactome.db
... The annotation push script is run nightly so this should appear in the repo tomorrow (April 21). ...
written 4 days ago by willem.ligtenberg120
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Comment: C: Change in pathway IDs scheme in reactome.db
... Did you verify this fixes your issue? These annotation packages are not tracked in version control. If this fixes your issue, I will ask Valerie is she can upload the version that I have on my website.   ...
written 4 days ago by willem.ligtenberg120
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Comment: C: Change in pathway IDs scheme in reactome.db
... Yes, you did get that right. You can download it here if you want to test drive it: https://owncloud.wligtenberg.nl/index.php/s/YfcW3XU19ptgrOR ...
written 6 days ago by willem.ligtenberg120
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Comment: C: Change in pathway IDs scheme in reactome.db
... Backwards compatibility, if you have a report (knitr/sweave) that might break now, if you were using the database ids to specifically look at a pathway. However, I do think that the main use case is starting at gene ids, finding related pathways (first pathway id, then the pathway name) that would s ...
written 6 days ago by willem.ligtenberg120
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Answer: A: Change in pathway IDs scheme in reactome.db
... No that change is not final. I was alerted to that issue last weekend. I have already created a new version which results in a one-to-one mapping of pathway-id to pathway name. Apparently, Reactome has changed their identifiers, and I have revised the way I am building the package. I mistakenly tho ...
written 6 days ago by willem.ligtenberg120
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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 7 weeks ago by willem.ligtenberg120
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Comment: C: Misleading information in reactome.db
... Thank you for the feedback, I will look into those issues. ...
written 7 weeks ago by willem.ligtenberg120
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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 7 weeks ago by willem.ligtenberg120

Latest awards to willem.ligtenberg

Scholar 12 months ago, created an answer that has been accepted. For A: reactome.db: reactome IDs not mapped to pathway names
Scholar 2.0 years ago, created an answer that has been accepted. For A: reactome.db: reactome IDs not mapped to pathway names

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