User: willem.ligtenberg

Reputation:
130
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Trusted
Location:
Netherlands
Website:
https://www.wligtenber...
Twitter:
wligtenberg
Last seen:
2 months, 1 week ago
Joined:
2 years, 8 months ago
Email:
w*****@wligtenberg.nl

Posts by willem.ligtenberg

<prev • 28 results • page 1 of 3 • next >
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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 9 weeks ago by willem.ligtenberg130
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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 3 months ago by willem.ligtenberg130
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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 3 months ago by willem.ligtenberg130
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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 months ago by willem.ligtenberg130
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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 3 months ago by willem.ligtenberg130
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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 3 months ago by willem.ligtenberg130
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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 3 months ago by willem.ligtenberg130
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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 3 months ago by willem.ligtenberg130
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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 3 months ago by willem.ligtenberg130
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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 4 months ago by willem.ligtenberg130

Latest awards to willem.ligtenberg

Scholar 16 months ago, created an answer that has been accepted. For A: reactome.db: reactome IDs not mapped to pathway names
Scholar 2.3 years ago, created an answer that has been accepted. For A: reactome.db: reactome IDs not mapped to pathway names

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