Bioconductor MSIGDB

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182

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geneset GeneSetEnrichment msigdb

4 weeks ago Seongsu • 0

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230

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msigdb gmt GSEA

written 6 weeks ago by Georg • 0

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626

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ssgsea GSVA biotype proteincoding msigdb

updated 5 months ago by Robert Castelo ★ 3.3k • written 5 months ago by snijesh ▴ 20

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1.2k

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msigdb GSEABase GSVA

updated 2.1 years ago by Robert Castelo ★ 3.3k • written 2.1 years ago by forlani.luca • 0

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1.9k

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gseabase msigdb genesetcollection Tutorial

written 5.9 years ago by t.kuilman ▴ 170

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4.0k

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clusterprofiler GSEA MSIGDB

updated 6.1 years ago by Guangchuang Yu ★ 1.2k • written 6.1 years ago by thomasjenner333 • 0

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1.4k

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limma romer msigdb

updated 8.7 years ago by James W. MacDonald 65k • written 8.7 years ago by Jon Manning ▴ 40

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1.3k

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category gostats msigdb hypergeometric test

8.8 years ago petyuk ▴ 70

8 results • Page 1 of 1

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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Votes

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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