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dozmorovlab / TADCompare

Package for analysis and characterization of differential TADs
https://dozmorovlab.github.io/TADCompare/
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Ontology Analysis vignette link not functional #12

Closed TerezaClarence closed 2 years ago

TerezaClarence commented 2 years ago

Dear TADCompare developers,

thank you for developing such an amazing tool! I was wondering whether there is any other link to the Ontology and pathway enrichment analysis? The link here on github for the Ontology pathway is not working.

Thank you very much.

Best regards, Tereza

mdozmorov commented 2 years ago

Thank you, Theresa, for noticing this. All vignettes are rendered on the Bioconductor page of TADcompare, https://bioconductor.org/packages/TADCompare/. Including the Gene Ontology Enrichment Analysis vignette. I updated the links in the README.

TerezaClarence commented 2 years ago

Thank you so much for your help. I am sorry to be bothering again but is there a simple way how to change/use a different reference genome within the rGREAT? for instance hg38 instead of hg19?

Thank you, Tereza

TerezaClarence commented 2 years ago

Actually, I found out it can be changed easily as suggested here: https://github.com/jokergoo/rGREAT however 'hg38' is not available as they wrote, only hg18 or hg19 for current versions,..