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Showing :
clusterProfiler
•
reset
1
vote
2
replies
67
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
1 day ago
Ana
• 0
2
votes
2
replies
135
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 days ago
julia_mcdonough
• 0
0
votes
1
reply
104
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 7 days ago by
Lucie
• 0
0
votes
1
reply
145
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
BCS12
• 0
0
votes
0
replies
117
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
12 days ago
andromeda
• 0
2
votes
1
reply
174
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 24 days ago by
Guido Hooiveld
★ 3.9k • written 26 days 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 28 days ago by
jandrade
• 0 • written 6.3 years ago by
Huang, Lei [BSD] - CRI
▴ 20
2
votes
2
replies
229
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
4 weeks ago
Eva
▴ 10
1
vote
7
replies
1.3k
views
enrichGOgradient color change
clusterProfiler
updated 4 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
inna.gur
• 0
1
vote
1
reply
171
views
Clsuter Profiler "counts"
enrich
clusterProfiler
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
mpluchs
• 0
2
votes
15
replies
625
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 9 weeks ago by
Michael Love
41k • written 9 weeks ago by
cinzia.spagnoli
• 0
0
votes
3
replies
375
views
Unable to install clusterProfiler
clusterProfiler
updated 8 weeks ago by
Perry
• 0 • written 10 weeks ago by
harsh
• 0
0
votes
2
replies
283
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
10 weeks ago
mello-vieira
• 0
0
votes
1
reply
248
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 12 weeks ago by
James W. MacDonald
65k • written 12 weeks ago by
Max
• 0
4
votes
2
replies
331
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 3 months ago by
sanchezsanchez
• 0
0
votes
3
replies
753
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
3
votes
6
replies
2.0k
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
0
votes
9
replies
597
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
4 months ago
nromerov
• 0
2
votes
9
replies
1.1k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler
HPO.db
updated 5 months ago by
Erqiang Hu
▴ 50 • written 5 months ago by
jovel_juan
▴ 30
3
votes
4
replies
1.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler
Annotationhub
updated 5 months ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
BS
• 0
0
votes
2
replies
445
views
Differential Expression Cutoffs for n = 1
clusterProfiler
DESeq2
6 months ago
georgii.vdovin
• 0
0
votes
0
replies
339
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler
DifferentialExpression
6 months ago
nromerov
• 0
0
votes
2
replies
600
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor
clusterProfiler
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
nilanjanamani88
• 0
1
vote
2
replies
805
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
7 months ago
Valéria
• 0
3
votes
2
replies
1.0k
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
0
votes
3
replies
1.2k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 5 months ago by
Fatemeh
• 0 • written 8 months ago by
Cen
• 0
0
votes
3
replies
1.4k
views
Not able to install clusterProfiler
clusterProfiler
updated 8 weeks ago by
Perry
• 0 • written 9 months ago by
Snehal
• 0
0
votes
0
replies
335
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
9 months ago
georgii.vdovin
• 0
2
votes
5
replies
3.1k
views
How to use EnrichGo of Cluster Profiler
EnrichGO
clusterProfiler
written 3.2 years ago by
Carolina
• 0
0
votes
1
reply
744
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
981
views
plot enrichment results
enrichplot
clusterProfiler
updated 9 months ago by
Lluís Revilla Sancho
▴ 730 • written 9 months ago by
Manuela
• 0
0
votes
2
replies
652
views
Question regarding FAQ
clusterProfiler
10 months ago
kl-fr
• 0
0
votes
0
replies
802
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
10 months ago
pg45863
▴ 10
2
votes
4
replies
1.4k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot
clusterProfiler
10 months ago
Tyroone
• 0
0
votes
1
reply
992
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler
AnnotationForge
updated 12 months ago by
shepherl
3.8k • written 12 months ago by
yuwt8920
• 0
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
12 months ago • updated 11 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 12 months ago by
Guido Hooiveld
★ 3.9k • written 12 months ago by
m-bihie
▴ 10
0
votes
1
reply
585
views
what does "exp1" mean in the gage() function?
gage
clusterProfiler
DESeq2
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
m-bihie
▴ 10
0
votes
3
replies
3.7k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 13 months ago by
Guido Hooiveld
★ 3.9k • written 14 months ago by
YNKIM
• 0
0
votes
1
reply
1.2k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler
enrichplot
updated 13 months ago by
Guido Hooiveld
★ 3.9k • written 13 months ago by
GenoMexa
• 0
0
votes
1
reply
724
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
ruiqi.li
• 0
4
votes
2
replies
4.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 13 months ago by
Erqiang Hu
▴ 50 • written 13 months ago by
redafazazi
• 0
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 13 months ago by
Basti
▴ 760 • written 13 months ago by
ruiqi.li
• 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 13 months ago by
ruiqi.li
• 0
0
votes
1
reply
642
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 15 months ago by
Michael Love
41k • written 15 months ago by
joanna
• 0
0
votes
2
replies
2.0k
views
clusterProfiler - custom annotations
clusterProfiler
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 16 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 16 months ago by
Basti
▴ 760 • written 16 months ago by
ghs101
• 0
1
vote
7
replies
1.4k
views
Adding geneID to list of gene locus IDs
cluster
OrgDb
clusterProfiler
written 17 months ago by
Chruut
• 0
2
votes
4
replies
2.1k
views
question regarding installation of "enrichplot" with BiocManager
R
BiocManager
install
clusterProfiler
GO
written 16 months ago by
abhisek001
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Input Question for deseq.r
by
ATpoint
★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present
by
ATpoint
★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded
by
ATpoint
★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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