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clusterProfiler
•
reset
1
vote
13
replies
278
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
4 days ago • updated 1 day ago
fernanda.backsouza
▴ 10
1
vote
3
replies
817
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 2 days ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
1
vote
1
reply
63
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
fernanda.backsouza
▴ 10
2
votes
2
replies
143
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
sansan
• 0
1
vote
2
replies
113
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
10 days ago
Ana
• 0
0
votes
1
reply
137
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 12 days ago by
Guido Hooiveld
★ 3.9k • written 15 days ago by
Lucie
• 0
2
votes
2
replies
170
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
14 days ago • updated 13 days ago
julia_mcdonough
• 0
0
votes
1
reply
164
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 18 days ago by
James W. MacDonald
65k • written 18 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
21 days ago • updated 20 days ago
andromeda
• 0
2
votes
1
reply
192
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 4 weeks ago by
Guido Hooiveld
★ 3.9k • written 4 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 5 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
2
votes
2
replies
244
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
5 weeks ago
Eva
▴ 10
1
vote
7
replies
1.4k
views
enrichGOgradient color change
clusterProfiler
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
inna.gur
• 0
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 10 weeks ago by
cinzia.spagnoli
• 0 • written 22 months ago by
AP
• 0
0
votes
3
replies
388
views
Unable to install clusterProfiler
clusterProfiler
updated 10 weeks ago by
Perry
• 0 • written 11 weeks ago by
harsh
• 0
0
votes
3
replies
1.4k
views
Not able to install clusterProfiler
clusterProfiler
updated 10 weeks ago by
Perry
• 0 • written 9 months ago by
Snehal
• 0
1
vote
1
reply
184
views
Clsuter Profiler "counts"
enrich
clusterProfiler
updated 10 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
mpluchs
• 0
2
votes
15
replies
663
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 10 weeks ago by
Michael Love
41k • written 11 weeks ago by
cinzia.spagnoli
• 0
0
votes
2
replies
299
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
11 weeks ago
mello-vieira
• 0
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 11 weeks ago by
Guido Hooiveld
★ 3.9k • written 3.2 years ago by
Alberto
• 0
0
votes
1
reply
259
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
346
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
1.9k
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 4 months ago by
EvaLan
• 0 • written 5.7 years ago by
bekah
▴ 40
0
votes
3
replies
787
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 4 months ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
Aastha Kapoor
• 0
0
votes
9
replies
628
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago • updated 4 months ago
nromerov
• 0
3
votes
6
replies
2.1k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 4 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
453
views
Differential Expression Cutoffs for n = 1
clusterProfiler
DESeq2
6 months ago
georgii.vdovin
• 0
0
votes
0
replies
352
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler
DifferentialExpression
6 months ago
nromerov
• 0
0
votes
2
replies
623
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
836
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler
emapplot
7 months ago
fluentin44
• 0
0
votes
2
replies
1.1k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
8 months ago • updated 7 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
3.9k
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
345
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
784
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 9 months ago by
Lluís Revilla Sancho
▴ 730 • written 10 months ago by
Manuela
• 0
0
votes
2
replies
673
views
Question regarding FAQ
clusterProfiler
10 months ago
kl-fr
• 0
3
votes
3
replies
4.6k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 10 months ago by
Guido Hooiveld
★ 3.9k • written 4.0 years ago by
t.b.kuipers
• 0
0
votes
0
replies
819
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 • updated 11 months ago
ruba-mahmoud
• 0
48 results • Page
1 of 1
Recent ...
Replies
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…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
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)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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