Bioconductor ClusterProfiler

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137

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clusterProfiler OrgDb biomaRt Zea_mays

updated 5 days ago by James W. MacDonald 65k • written 6 days ago by sansan • 0

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110

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clusterProfiler GeneSetEnrichment

8 days ago Ana • 0

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KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware

updated 1 day ago by James W. MacDonald 65k • written 1 day ago by fernanda.backsouza ▴ 10

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159

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clusterProfiler ggpubr

updated 16 days ago by James W. MacDonald 65k • written 17 days ago by BCS12 • 0

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166

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Pathways clusterProfiler gseKEGG KEGG

12 days ago julia_mcdonough • 0

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129

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clusterProfiler gseKEGG

19 days ago andromeda • 0

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130

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DOSE enrichplot clusterProfiler

updated 10 days ago by Guido Hooiveld ★ 3.9k • written 14 days ago by Lucie • 0

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809

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clusterProfiler RNASeq

updated 16 hours ago by Guangchuang Yu ★ 1.2k • written 13 months ago by ruiqi.li ▴ 10

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236

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clusterProfiler GenomicDistributionsData KEGG

3 days ago • updated 5 hours ago fernanda.backsouza ▴ 10

9 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

Answer: How to retrieve gene ontology GO class from gene list?

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

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