Bioconductor Clusterprofiler

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106

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KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware

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

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383

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clusterProfiler GenomicDistributionsData KEGG

12 days ago • updated 9 days ago fernanda.backsouza ▴ 10

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183

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clusterProfiler OrgDb biomaRt Zea_mays

updated 14 days ago by James W. MacDonald 65k • written 15 days ago by sansan • 0

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133

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clusterProfiler GeneSetEnrichment

17 days ago Ana • 0

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189

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Pathways clusterProfiler gseKEGG KEGG

21 days ago julia_mcdonough • 0

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157

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DOSE enrichplot clusterProfiler

updated 19 days ago by Guido Hooiveld ★ 3.9k • written 23 days ago by Lucie • 0

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179

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clusterProfiler ggpubr

updated 25 days ago by James W. MacDonald 65k • written 26 days ago by BCS12 • 0

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143

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clusterProfiler gseKEGG

28 days ago andromeda • 0

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854

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clusterProfiler RNASeq

updated 9 days ago by Guangchuang Yu ★ 1.2k • written 14 months ago by ruiqi.li ▴ 10

9 results • Page 1 of 1

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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. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

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…

Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0

Thank you Tim, this is a great help in getting me started!

Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k

Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…

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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

A: Print Differentially Expressed Exons From Dexseq Results

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