Showing : enrichment analysis • reset
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Find genes in pathways enrichment
dmrcate enrichment analysis epic array goregion missmethyl
updated 4.2 years ago by ▴ 20 • written 5.2 years ago by ▴ 10
6
votes
6
replies
6.1k
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Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 50
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1.4k
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Error using gosummaries (GOsummaries) on small log2 fold change values
gosummaries gene ontology enrichment analysis
7.6 years ago jan.soderman • 0
3
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2
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7.1k
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Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.8 years ago by ★ 1.2k • written 7.9 years ago by ▴ 10
2
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5
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4.6k
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GO enrichment comparison with other programs
clusterprofiler enrichment analysis
updated 8.7 years ago by ★ 1.2k • written 8.7 years ago by ▴ 40
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0
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2.0k
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Leading edge analysis
leading edge analysis enrichment analysis
9.0 years ago Adrian Johnson ▴ 330
9
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6
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7.0k
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GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 20
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1.6k
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Create list of genes within each GOslim term
gene ontology goslim enrichment analysis gene annotation
9.4 years ago mirko • 0
8 results • Page 1 of 1
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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Exactly, MDS was computed on logCPM values from `cpm(x, log=TRUE)` after running `calcNormFactors(method="TMMwsp")` on the DGE object. I al…
Answer: GO.db and others package Download failure by James W. MacDonald 68k
You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
MDS of what quantity? LogCPM from `cpm()`? I don't have a definitive answer, but my feeling that is that library size effects are to be ex…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Apologies for not clarifying earlier, you're right: it is a PCA, not an MDS. In local machine, computing the MDS takes quite a long time, P…
Answer: replace cat with message in glmTreat when lfc = 0 by Gordon Smyth 53k
Yes, I agree that the message should be a `message` rather than `cat` output, and the message is perhaps not needed at all, because anyone …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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