User: willem.ligtenberg

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150
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Location:
Netherlands
Website:
https://www.wligtenber...
Twitter:
wligtenberg
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2 weeks, 5 days ago
Joined:
3 years ago
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Posts by willem.ligtenberg

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: p
... That is a good suggestion, although I don't know how to make an annotation package available in devel. The are treated a but differently from the normal packages, as they are not in git. But I am sure, we can figure that out.   ...
written 26 days ago by willem.ligtenberg150
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Answer: A: Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: p
... As the creator of reactome.db, I could support a uniprot to reactome pathway mapping in my package. However, we are past feature freeze in this release cycle. This would mean that this addition would only be available in half a year. Obviously, I could make it available somewhere else, but it would ...
written 26 days ago by willem.ligtenberg150
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Comment: C: reactome.db installation problem
... This is highly unlikely to be related to the package. Did you try to install it on another machine? What filesystem is the disk you are trying to install to? I notice you are on linux, but if you are writhing to a shared disk between windows and linux (FAT/NTFS) you might run into path length issues ...
written 6 months ago by willem.ligtenberg150
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Comment: C: Change in pathway IDs scheme in reactome.db
... I mailed Valerie an updated package with the version number increase. ...
written 7 months ago by willem.ligtenberg150
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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 7 months ago by willem.ligtenberg150
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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 7 months ago by willem.ligtenberg150
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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 7 months ago by willem.ligtenberg150
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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 7 months ago by willem.ligtenberg150
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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 7 months ago by willem.ligtenberg150
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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 7 months ago by willem.ligtenberg150

Latest awards to willem.ligtenberg

Scholar 19 months ago, created an answer that has been accepted. For A: reactome.db: reactome IDs not mapped to pathway names
Scholar 2.6 years ago, created an answer that has been accepted. For A: reactome.db: reactome IDs not mapped to pathway names

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