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4
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4
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3.7k
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Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 29 days ago by • 0 • written 6.3 years ago by ▴ 20
1
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2
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745
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 12 hours ago by • 0 • written 13 months ago by ▴ 10
2
votes
1
reply
175
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 25 days ago by ★ 3.9k • written 27 days ago by ▴ 10
2
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2
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148
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
6 days ago julia_mcdonough • 0
0
votes
1
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146
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How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 10 days ago by 65k • written 11 days ago by • 0
0
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0
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122
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
13 days ago andromeda • 0
0
votes
1
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110
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compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 4 days ago by ★ 3.9k • written 8 days ago by • 0
1
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2
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76
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
2 days ago Ana • 0
1
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1
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41
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OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 10 hours ago by ★ 3.9k • written 10 hours ago by • 0
9 results • Page 1 of 1
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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