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Reviewing the annotation intersection violations alerted us to:
https://amigo.geneontology.org/amigo/reference/PMID:12485443
This paper describes plasma membrane lipid profiling, and as such isn't…
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Dear Dr. Howrigan.
Could I ask another detailed method about you paper. In gene set enrichment section, you used binom.test and prop.test, and calculated proportion ratio of case genes in specific …
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**Is your feature request related to a problem? Please describe.**
gene set enrichment analysis - GO term analysis
**Describe the solution you'd like**
similar to rnfuzzy or IRIS: extend the tabl…
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Hi,
I performed the enrichment analysis using my background set, and repeated it restricting the background set to only include genes with at least one annotation term (based on annotation file tha…
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Reading to provide background information about existing large gene set curation projects and how they are used in enrichment analyses to improve the interpretation of large genomic datasets.
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Need tutorials for general level classification and then a more detailed example for one subclass.
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Hi,
I was trying to run the GSEA function and got confused with its parameters `exponent`, which is documented as `weight of each step`.
```
GSEA(
geneList,
exponent = 1,
minGSSize = 1…
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I come from China, I am using the FUMA for gene set enrichment, but FUMA not respond to my uploaded gene list (I tried to ENSEMBL ID/gene symbol). What is wrong has happened? Is FUMA running well now?
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HI Team 11,
Great proposal! Here are some of my feedback and thoughts on it:
1. How is your initial DE analysis going to be different from the original study? What was the pipeline they used and…
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## Pathway analysis
### Data
- [x] Genes from PND8 vs PND15 (using `t-value`)
- [x] Genes from PND14 vs PNW8 (using `logFC`)
### GO database
- [x] GO BP
- [x] GO CC
- [x] GO MF
### Metho…