Bioconductor ClusterProfiler

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858

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clusterProfiler RNASeq

updated 10 days ago by Guangchuang Yu ★ 1.2k • written 14 months ago by ruiqi.li ▴ 10

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395

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clusterProfiler GenomicDistributionsData KEGG

13 days ago • updated 10 days ago fernanda.backsouza ▴ 10

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191

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Pathways clusterProfiler gseKEGG KEGG

22 days ago julia_mcdonough • 0

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187

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clusterProfiler OrgDb biomaRt Zea_mays

updated 15 days ago by James W. MacDonald 65k • written 16 days ago by sansan • 0

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180

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clusterProfiler ggpubr

updated 26 days ago by James W. MacDonald 65k • written 27 days ago by BCS12 • 0

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157

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DOSE enrichplot clusterProfiler

updated 20 days ago by Guido Hooiveld ★ 3.9k • written 24 days ago by Lucie • 0

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143

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clusterProfiler gseKEGG

29 days ago andromeda • 0

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137

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clusterProfiler GeneSetEnrichment

18 days ago Ana • 0

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110

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KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware

updated 11 days ago by James W. MacDonald 65k • written 11 days ago by fernanda.backsouza ▴ 10

9 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…

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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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