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Showing :
clusterprofiler
•
reset
2
votes
13
replies
403
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
14 days ago • updated 11 days ago
fernanda.backsouza
▴ 10
1
vote
3
replies
861
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 12 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
1
reply
111
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 12 days ago by
James W. MacDonald
65k • written 13 days ago by
fernanda.backsouza
▴ 10
2
votes
2
replies
190
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
sansan
• 0
1
vote
2
replies
140
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
20 days ago
Ana
• 0
0
votes
1
reply
159
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 22 days ago by
Guido Hooiveld
★ 3.9k • written 25 days ago by
Lucie
• 0
2
votes
2
replies
193
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
24 days ago • updated 23 days ago
julia_mcdonough
• 0
0
votes
1
reply
180
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
BCS12
• 0
0
votes
0
replies
148
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
4 weeks ago
andromeda
• 0
2
votes
1
reply
212
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 6 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 weeks ago by
enee
▴ 10
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 6 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
2
votes
2
replies
261
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
7 weeks ago • updated 6 weeks ago
Eva
▴ 10
1
vote
7
replies
1.5k
views
enrichGOgradient color change
clusterProfiler
updated 7 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
inna.gur
• 0
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 11 weeks ago by
cinzia.spagnoli
• 0 • written 23 months ago by
AP
• 0
0
votes
3
replies
418
views
Unable to install clusterProfiler
clusterProfiler
updated 11 weeks ago by
Perry
• 0 • written 12 weeks ago by
harsh
• 0
0
votes
3
replies
1.5k
views
Not able to install clusterProfiler
clusterProfiler
updated 11 weeks ago by
Perry
• 0 • written 9 months ago by
Snehal
• 0
1
vote
1
reply
200
views
Clsuter Profiler "counts"
enrich
clusterProfiler
updated 11 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
mpluchs
• 0
2
votes
15
replies
702
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 12 weeks ago by
Michael Love
41k • written 12 weeks ago by
cinzia.spagnoli
• 0
0
votes
2
replies
320
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
3 months ago
mello-vieira
• 0
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 3.3 years ago by
Alberto
• 0
0
votes
1
reply
278
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Max
• 0
4
votes
2
replies
366
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 3 months ago by
sansan
• 0
0
votes
6
replies
8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler
r
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 7.3 years ago by
prp291
• 0
0
votes
2
replies
2.1k
views
clusterProfiler - custom annotations
clusterProfiler
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 16 months ago by
adam
• 0
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
1.5k
views
ClusterProfiler - enrichKEGG on specific pathways
kegg
enrichkegg
clusterprofiler
updated 5 months ago by
EvaLan
• 0 • written 5.8 years ago by
bekah
▴ 40
0
votes
3
replies
823
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 5 months ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
Aastha Kapoor
• 0
0
votes
9
replies
666
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago
nromerov
• 0
3
votes
6
replies
2.1k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by
James W. MacDonald
65k • written 18 months ago by
Susanne
▴ 10
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler
HPO.db
updated 6 months ago by
Erqiang Hu
▴ 50 • written 6 months ago by
jovel_juan
▴ 30
3
votes
4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler
Annotationhub
updated 6 months ago by
Guido Hooiveld
★ 3.9k • written 6 months ago by
BS
• 0
0
votes
3
replies
1.3k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 6 months ago by
Fatemeh
• 0 • written 8 months ago by
Cen
• 0
0
votes
2
replies
473
views
Differential Expression Cutoffs for n = 1
clusterProfiler
DESeq2
6 months ago
georgii.vdovin
• 0
0
votes
0
replies
370
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler
DifferentialExpression
6 months ago
nromerov
• 0
0
votes
2
replies
651
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor
clusterProfiler
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
nilanjanamani88
• 0
1
vote
2
replies
865
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler
emapplot
8 months ago • updated 7 months ago
fluentin44
• 0
0
votes
2
replies
1.2k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
8 months ago
Valéria
• 0
3
votes
2
replies
1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 8 months ago by
Guido Hooiveld
★ 3.9k • written 8 months ago by
Milan
▴ 10
2
votes
2
replies
4.0k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 9 months ago by
Trinh
• 0 • written 7.8 years ago by
mdtorohernando
▴ 10
0
votes
0
replies
354
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
9 months ago
georgii.vdovin
• 0
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO
clusterProfiler
written 3.3 years ago by
Carolina
• 0
0
votes
1
reply
808
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
manuelsokolov
• 0
0
votes
5
replies
1.0k
views
plot enrichment results
enrichplot
clusterProfiler
updated 10 months ago by
Lluís Revilla Sancho
▴ 730 • written 10 months ago by
Manuela
• 0
0
votes
2
replies
690
views
Question regarding FAQ
clusterProfiler
10 months ago
kl-fr
• 0
3
votes
3
replies
4.7k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 11 months ago by
Guido Hooiveld
★ 3.9k • written 4.0 years ago by
t.b.kuipers
• 0
0
votes
0
replies
842
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
11 months ago
pg45863
▴ 10
2
votes
4
replies
1.5k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot
clusterProfiler
11 months ago
Tyroone
• 0
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
12 months ago
ruba-mahmoud
• 0
0
votes
1
reply
1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler
AnnotationForge
updated 12 months ago by
shepherl
3.9k • written 12 months ago by
yuwt8920
• 0
0
votes
2
replies
8.9k
views
Clusterprofiler error: No gene can be mapped
software error
go
annotation
clusterProfiler
updated 12 months ago by
tarltonuk2089
• 0 • written 4.1 years ago by
tianshenbio
• 0
50 results • Page
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Answer: How to save the DEXSeq results
by
Michael Love
41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups
by
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★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
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65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
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by
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41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways"
by
Michael Love
41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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