Bioconductor Kegg.db

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KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT

updated 4.6 years ago by James W. MacDonald 67k • written 4.6 years ago by tobias-messmer ▴ 20

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KEGG kegg.db kegggraph

6.7 years ago Raymond ▴ 20

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pfam go.db kegg.db

updated 7.1 years ago by Martin Morgan 25k • written 7.1 years ago by josefina.lascanomaillard • 0

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affy annaffy go.db kegg.db

updated 7.6 years ago by James W. MacDonald 67k • written 7.6 years ago by Angela • 0

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software error download.kegg() kegg.db use_internal_data = FALSE

updated 8.3 years ago by Guangchuang Yu ★ 1.2k • written 8.3 years ago by happylittlepig • 0

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KEGG.db KEGG id

updated 9.6 years ago by Martin Morgan 25k • written 9.6 years ago by NS ▴ 60

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Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0

> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…

Comment: EuroBioC2024 abstract submission is open! by Esperan • 0

Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…

Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k

I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…

Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0

Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…

Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k

I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …

Votes

Answer: How do I merge a list of GRanges?

A: p.adjust BH generates duplicate values

Answer: Adjusted p-values become NA when sub-setting samples

Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice

Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim

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