R package for GO-BP enrichment analysis with c(symbol, log2foldchange, pvalue)
Hello everyone.
I am trying to get mmu GO-BP pathways from mRNA deseq2 data from mouse:
Here is input data:
input_genes
# Symbol log2FoldChange.case.control. Padj
#1 Cnn2 -1.024326 9.830000e-67
#2 Prkg2 -2.702457 8.240000e-32
As you can see i have gene symbol, log2foldchange, and padj data. Which R package can i use it for mmu GO-BP analysis? I tried topGO but this input data not enough for that.
Is there any alternative R package for mouse GO-BP analysis based on these 3 column?
Thank you so much
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What do you mean by "this input data is not enough" for topGO. As far as I'm aware topGO just requires a list of differentially expressed genes?
Anyway, for GO analysis of RNA-seq data I would always recommend goseq.