Bioconductor GSEA

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6.6k

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GSEA GeneSetEnrichment DifferentialExpression

updated 3 months ago by ATpoint ★ 4.1k • written 2.1 years ago by nhaus ▴ 30

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1.3k

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enrichplot GSEA clusterProfiler

updated 6 months ago by Fatemeh • 0 • written 9 months ago by Cen • 0

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989

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GSEA voom limma

updated 10 months ago by Gordon Smyth 50k • written 10 months ago by manuelsokolov • 0

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623

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GSEA fgsea

9 months ago Cen • 0

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611

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gsea DESeq2

updated 6 months ago by ATpoint ★ 4.1k • written 6 months ago by Grace.Ciabattoni • 0

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359

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fgsea gsea

6 weeks ago • updated 4 weeks ago Gordon • 0

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235

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msigdb gmt GSEA

written 7 weeks ago by Georg • 0

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215

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clusterProfiler annotation gseGO gsea OrgDb

updated 6 weeks ago by Guido Hooiveld ★ 3.9k • written 6 weeks ago by enee ▴ 10

8 results • Page 1 of 1

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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k

I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?

Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k

If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…

Comment: Memory errors using read.bismark? by Juan Higareda • 0

Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…

Answer: meffil.snp.concordance by James W. MacDonald 65k

This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…

Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k

Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…

Votes

Answer: How to save the DEXSeq results

Answer: minfi support of illumina Infinium methylationEPIC v2.0

Comment: minfi support of illumina Infinium methylationEPIC v2.0

Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it

Comment: Help with running egsea()

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