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MaayanLab / Playbook-Workflow-Builder

A repository for the Playbook Workflow Builder project.
https://playbook-workflow-builder.cloud
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STRING and Wikipathways Nodes #237

Open reductiveminded opened 2 weeks ago

reductiveminded commented 2 weeks ago

Description: After uploading a gene counts matrix and corresponding metadata file, I performed DE analysis, then created a list of up and down scored genes. For each list I performed STRING and Wikipathways analysis to see which genes were connected / enriched pathways. For some reason every time I do this it returns 0 values. If I take the same list and perform the enrichment analysis online at the respective websites it shows me a totally different output (with many connections, that of which are highly connected)

reductiveminded commented 2 weeks ago

If I instead upload a gene list (from say another publication) it works totally fine. It seems to be only from the particular counts and metadata files I uploaded.

u8sand commented 2 weeks ago

Are you able to share the link to your playbook with us so we can investigate?

reductiveminded commented 2 weeks ago

https://playbook-workflow-builder.cloud/report/2537ac09-7b02-100a-40d9-20c47e4ec1d4

reductiveminded commented 1 week ago

Hello, Is there any update regarding this yet? My final presentation is in 2 weeks and I am really hoping that the STRING outputs will work :) Thanks!