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When using ```GSEABase::getGmt()```, a common function for reading in GMT files, I get an error saying that each ```setName``` must be distinct. This refers to column ```V1``` in the attached screensh…
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https://nbviewer.jupyter.org/github/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb
and binder: https://hub.gke.mybinder.org/user/biolink-ontobio-actww75g/notebooks/notebooks/Pheno…
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Hi,
I love the concept of your tool, and am wondering if it would be appropriate to use in a more special l case. I want to evaluate haplotype-resolved de-novo assemblies of a complex region, and I h…
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### **Describe the bug**
When running `decoupler` to infer transcription factor activities using `dc.run_ulm` and pathway activities using `dc.run_mlm`, I encounter an incompatibility issue with `pyp…
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Hi Tobias,
Thank you for creating the ITAG4.1 GO annotation for tomato! This is a valuable resource for the plant research community.
I am currently using your annotation to perform GO enric…
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We have different ways to name a few major properties, and for downstream code it would be very helpful to harmonise:
**1) Name of the property for content item unique identifier**
- in topic assi…
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#### Description
Skipping a flaky test `CTI Enrichment Displays enrichment matched.* fields on the timeline Displays enrichment matched.* fields on the timeline` in this PR: https://github.com/elas…
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### Prerequisites
Dear YuLab-SMU
I am trying to apply the GO enrichment to the results obtained in WGCNA. I was not able to get the data idirectly into R, so I did the manual list on excel of the…
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I am having some questions about the `enrichGO` function, and its comparability with the results obtained from the `topGO` package. I'd appreciate if someone can comment on my questions, I think this …
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Hi!
In performing gene set enrichment analysis on DSS output, how do I generate a background set? I tried setting the p.threshold in callDMR to 1.0 but I'm not sure if this is the right approach.
…