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Showing :
clusterProfiler
•
reset
0
votes
4
replies
106
views
error running enricher from clusterprofiler
clusterProfiler
cluster
1 day ago
Yael
• 0
0
votes
1
reply
103
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 3 days ago by
Guido Hooiveld
★ 4.0k • written 4 days ago by
aogunbaw
• 0
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
fernanda.backsouza
▴ 10
2
votes
13
replies
475
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
25 days ago • updated 22 days ago
fernanda.backsouza
▴ 10
2
votes
2
replies
209
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
sansan
• 0
1
vote
2
replies
166
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
4 weeks ago
Ana
• 0
2
votes
2
replies
212
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
4 weeks ago
julia_mcdonough
• 0
0
votes
1
reply
193
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 weeks ago by
Guido Hooiveld
★ 4.0k • written 5 weeks ago by
Lucie
• 0
0
votes
1
reply
187
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
BCS12
• 0
0
votes
0
replies
161
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
5 weeks ago
andromeda
• 0
2
votes
1
reply
229
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 7 weeks ago by
enee
▴ 10
2
votes
2
replies
286
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
8 weeks ago
Eva
▴ 10
1
vote
1
reply
208
views
Clsuter Profiler "counts"
enrich
clusterProfiler
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
mpluchs
• 0
2
votes
15
replies
729
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 3 months ago by
Michael Love
42k • written 3 months ago by
cinzia.spagnoli
• 0
0
votes
3
replies
448
views
Unable to install clusterProfiler
clusterProfiler
updated 3 months ago by
Perry
• 0 • written 3 months ago by
harsh
• 0
0
votes
2
replies
350
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
3 months ago
mello-vieira
• 0
0
votes
1
reply
308
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
386
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 4 months ago by
Guido Hooiveld
★ 4.0k • written 4 months ago by
sansan
• 0
0
votes
3
replies
877
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
★ 4.0k • written 5 months ago by
Aastha Kapoor
• 0
0
votes
9
replies
701
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago
nromerov
• 0
1
vote
7
replies
1.6k
views
enrichGOgradient color change
clusterProfiler
updated 8 weeks ago by
Guido Hooiveld
★ 4.0k • written 6 months ago by
inna.gur
• 0
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
★ 4.0k • written 6 months ago by
BS
• 0
0
votes
2
replies
493
views
Differential Expression Cutoffs for n = 1
clusterProfiler
DESeq2
7 months ago
georgii.vdovin
• 0
0
votes
0
replies
385
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler
DifferentialExpression
7 months ago
nromerov
• 0
0
votes
2
replies
676
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
898
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler
emapplot
8 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 9 months ago by
Guido Hooiveld
★ 4.0k • written 9 months ago by
Milan
▴ 10
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 9 months ago by
Cen
• 0
0
votes
3
replies
1.5k
views
Not able to install clusterProfiler
clusterProfiler
updated 3 months ago by
Perry
• 0 • written 10 months ago by
Snehal
• 0
0
votes
0
replies
358
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
10 months ago
georgii.vdovin
• 0
0
votes
1
reply
857
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
manuelsokolov
• 0
0
votes
5
replies
1.1k
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
702
views
Question regarding FAQ
clusterProfiler
11 months ago
kl-fr
• 0
0
votes
0
replies
863
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
11 months ago
pg45863
▴ 10
2
votes
4
replies
1.6k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot
clusterProfiler
11 months ago
Tyroone
• 0
0
votes
1
reply
1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler
AnnotationForge
updated 13 months ago by
shepherl
3.9k • written 13 months ago by
yuwt8920
• 0
0
votes
5
replies
1.4k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
13 months ago • updated 12 months ago
ruba-mahmoud
• 0
1
vote
3
replies
1.1k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 13 months ago by
Guido Hooiveld
★ 4.0k • written 13 months ago by
m-bihie
▴ 10
0
votes
1
reply
607
views
what does "exp1" mean in the gage() function?
gage
clusterProfiler
DESeq2
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
m-bihie
▴ 10
0
votes
1
reply
1.2k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler
enrichplot
updated 14 months ago by
Guido Hooiveld
★ 4.0k • written 14 months ago by
GenoMexa
• 0
1
vote
3
replies
886
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 22 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
4
votes
2
replies
4.5k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 14 months ago by
Erqiang Hu
▴ 50 • written 14 months ago by
redafazazi
• 0
1
vote
7
replies
1.9k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 14 months ago by
Basti
▴ 780 • written 14 months ago by
ruiqi.li
▴ 10
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 4 months ago by
Guido Hooiveld
★ 4.0k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
3
replies
4.0k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 14 months ago by
Guido Hooiveld
★ 4.0k • written 15 months ago by
YNKIM
• 0
0
votes
1
reply
671
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 15 months ago by
Michael Love
42k • written 16 months ago by
joanna
• 0
0
votes
2
replies
2.2k
views
clusterProfiler - custom annotations
clusterProfiler
updated 4 months ago by
Guido Hooiveld
★ 4.0k • written 17 months ago by
adam
• 0
1
vote
1
reply
1.1k
views
How to include background "universe" in compareCluster function of clusterprofiler package
clusterProfiler
updated 17 months ago by
Basti
▴ 780 • written 17 months ago by
ghs101
• 0
50 results • Page
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Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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