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ClusterProfiler
•
reset
1
vote
13
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302
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Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
5 days ago • updated 2 days ago
fernanda.backsouza
▴ 10
1
vote
3
replies
820
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 3 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
1
reply
68
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 3 days ago by
James W. MacDonald
65k • written 4 days ago by
fernanda.backsouza
▴ 10
2
votes
2
replies
145
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
sansan
• 0
1
vote
2
replies
115
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
11 days ago
Ana
• 0
0
votes
1
reply
138
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 13 days ago by
Guido Hooiveld
★ 3.9k • written 16 days ago by
Lucie
• 0
2
votes
2
replies
174
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
15 days ago • updated 14 days ago
julia_mcdonough
• 0
0
votes
1
reply
166
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
BCS12
• 0
0
votes
0
replies
134
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
22 days ago • updated 21 days ago
andromeda
• 0
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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