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ClusterProfiler
•
reset
1
vote
13
replies
14k
views
GeneList issue ClusterProfiler
genelist
clusterprofiler
6.9 years ago
bhgyu
▴ 30
2
votes
10
replies
12k
views
keytype not supported in clusterprofiler when it is ensembl IDs?
clusterProfiler
enrichGO
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
kavator
▴ 30
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA
clusterProfiler
6.5 years ago
giuseppe0525
• 0
0
votes
1
reply
9.3k
views
"No genes can be mapped...." using enrichGO in clusterProfiler
R
TAIR
clusterProfiler
enrichGO
Arabidopsis
updated 3.0 years ago by
Guido Hooiveld
★ 3.9k • written 3.0 years ago by
abby-s
• 0
0
votes
5
replies
9.3k
views
Cannot install clusterProfiler
clusterprofiler
biocinstaller
updated 2.4 years ago by
thkapell
▴ 10 • written 6.0 years ago by
dtatarak
• 0
8
votes
9
replies
8.9k
views
Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'
get_fun_from_pkg
clusterProfiler
rvcheck
updated 2.4 years ago by
Samanwoy
• 0 • written 2.6 years ago by
R user Muuchi
• 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
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
6
votes
11
replies
7.8k
views
Cluster profiler - KEGG analysis
clusterprofiler
3.8 years ago
sunnykevin97
• 0
1
vote
2
replies
7.6k
views
ENSEMBL to ENTREZ ID
clusterProfiler
22 months ago
martacrespi7
• 0
0
votes
3
replies
7.4k
views
clusterProfiler - how does showCategory work in dotplot from compareClusterResult class?
clusterprofiler
7.5 years ago
Jane Merlevede
▴ 90
2
votes
4
replies
7.4k
views
What's the difference between p.adjust and qvalue?
clusterprofiler
updated 6.9 years ago by
Guido Hooiveld
★ 3.9k • written 6.9 years ago by
tjiagoM
▴ 10
2
votes
11
replies
7.2k
views
ClusterProfiler enrichGO function leads to different enrichment results in different computers, while the code and gene list keep same
clusterProfiler
2.4 years ago
liuzhy
▴ 10
0
votes
6
replies
7.1k
views
question on GO analysis using clusterProfiler
clusterprofiler
geneontology
updated 6.5 years ago by
thokall
▴ 160 • written 6.5 years ago by
giuseppe0525
• 0
4
votes
4
replies
6.9k
views
what the test method for enrichGO in clusterProfiler?
clusterProfiler
2.4 years ago
xiaofeiwang18266
▴ 50
4
votes
2
replies
6.7k
views
How to export enrichGO results for future visualization with barplot, dotplot, emapplot...
clusterprofiler
enrichGO
barplot
dotplot
5.7 years ago
MAP
• 0
4
votes
10
replies
6.2k
views
Help with enrichKEGG function in clusterProfiler
clusterprofiler
updated 21 months ago by
Nitish Kumar Mishra
▴ 40 • written 8.2 years ago by
1992
▴ 10
4
votes
1
reply
6.0k
views
Warning message as converting gene Symbol to ENTREZID
go
clusterprofiler
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
adR
▴ 30
1
vote
4
replies
6.0k
views
ClusterProfiler - How to : input file, groupGo, enrichGo
clusterprofiler
input files
error
help
updated 7.2 years ago by
Guangchuang Yu
★ 1.2k • written 7.2 years ago by
Mataivic
• 0
3
votes
1
reply
5.9k
views
clusterProfiler - Non model organism
clusterprofiler
updated 6.5 years ago by
Guangchuang Yu
★ 1.2k • written 6.5 years ago by
rozanskide
▴ 10
0
votes
5
replies
5.7k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler
pathway analysis
pathways
updated 18 months ago by
yuhang
• 0 • written 5.9 years ago by
Mr.RB
▴ 20
1
vote
2
replies
5.6k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler
DOSE
updated 16 months ago by
Nick O
• 0 • written 20 months ago by
ummscr
• 0
0
votes
2
replies
5.1k
views
failing to install the package clusterProfiler in R (version 3.4.1)
clusterprofiler
updated 6.4 years ago by
Guangchuang Yu
★ 1.2k • written 6.4 years ago by
fengleiluck
• 0
0
votes
3
replies
5.0k
views
ridgeplot doesn't work: Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero
clusterProfiler
updated 19 months ago by
mttrantrietminh
• 0 • written 21 months ago by
Y.K
• 0
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 12 weeks ago by
Guido Hooiveld
★ 3.9k • written 3.2 years ago by
Alberto
• 0
3
votes
2
replies
4.8k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa
pathway analysis
enrichment analysis
clusterprofiler
updated 6.5 years ago by
Guangchuang Yu
★ 1.2k • written 6.5 years ago by
Miguel.Cosenza
▴ 10
1
vote
4
replies
4.8k
views
ClusterProfiler: enrichGO / compareCluster and Pvalue threeshold
clusterprofiler
updated 9.0 years ago by
Guangchuang Yu
★ 1.2k • written 9.0 years ago by
samuel collombet
▴ 140
3
votes
3
replies
4.7k
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
6
replies
4.6k
views
enrichMKEGG can not identify the species
clusterprofiler
updated 5.8 years ago by
Guido Hooiveld
★ 3.9k • written 5.8 years ago by
bright602
• 0
1
vote
2
replies
4.5k
views
clusterProfiler : How works the q-value filtering ? What is a good cutoff ? Is this like an FDR ?
clusterprofiler
qvalue
updated 7.5 years ago by
Guangchuang Yu
★ 1.2k • written 7.5 years ago by
ZheFrench
▴ 50
2
votes
3
replies
4.5k
views
No gene set have size > 10 ...
clusterprofiler
gene ontology
5.5 years ago
anton.kratz
▴ 60
3
votes
7
replies
4.5k
views
clusterProfiler - GeneRatio & nb of genes always positively correlated in dotplot
clusterProfiler
7.5 years ago
Jane Merlevede
▴ 90
4
votes
2
replies
4.4k
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
0
votes
9
replies
4.4k
views
What does "level" argument mean in groupGO function (cluster profiler)?
clusterprofiler
go
groupGO
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
b.nota
▴ 360
2
votes
2
replies
4.3k
views
How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
ggplot2
clusterprofiler
visualization
gseGo
7.1 years ago • updated 3.5 years ago
tcalvo
▴ 90
6
votes
2
replies
4.3k
views
help with clusterProfiler enricher function
clusterprofiler
8.0 years ago
naholi.alejandri
▴ 50
0
votes
5
replies
4.3k
views
odd results "No enrichment found in any of gene cluster"
clusterprofiler
updated 6.9 years ago by
Guangchuang Yu
★ 1.2k • written 6.9 years ago by
joseph
▴ 50
4
votes
4
replies
4.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler
reactomepa
dose
updated 18 months ago by
12133067
• 0 • written 7.7 years ago by
enricoferrero
▴ 660
0
votes
2
replies
4.2k
views
Understanding clusterprofiler enrichment results
clusterprofiler
gene set enrichment analysis
enricher
sc-rnaseq
updated 5.8 years ago by
Guangchuang Yu
★ 1.2k • written 5.8 years ago by
atakanekiz
▴ 30
5
votes
13
replies
4.2k
views
Getting error
enrichplot
clusterProfiler
org.Hs.eg.db
updated 2.1 years ago by
793345316
▴ 40 • written 2.1 years ago by
beslinail
• 0
8
votes
5
replies
4.1k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler
enrichplot
5.0 years ago • updated 23 months ago
charles.foster
▴ 160
2
votes
2
replies
4.0k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler
GSEA
MSIGDB
updated 6.1 years ago by
Guangchuang Yu
★ 1.2k • written 6.1 years ago by
thomasjenner333
• 0
0
votes
1
reply
4.0k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler
ReactomePA
updated 4.1 years ago by
Guangchuang Yu
★ 1.2k • written 4.1 years ago by
liampvmartin1992
▴ 10
1
vote
4
replies
4.0k
views
Issues with scaling down enrichplot's dotplot and gseaplot2 plots
RNASeq
clusterProfiler
enrichplot
updated 2.1 years ago by
Lihe
• 0 • written 2.8 years ago by
jiro.becker
• 0
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
1
vote
10
replies
4.0k
views
Issue of clusterprofiler package
clusterprofiler
updated 7.5 years ago by
Guangchuang Yu
★ 1.2k • written 7.5 years ago by
unique379
• 0
3
votes
4
replies
3.9k
views
Sort clusterProfiler result
clusterProfiler
sort
updated 6.8 years ago by
sghoshucla
• 0 • written 8.7 years ago by
horcsct
▴ 10
0
votes
2
replies
3.9k
views
ClusterProfiler dotplot mapping fold change to colour of dots
clusterProfiler
updated 18 months ago by
Javier
• 0 • written 2.1 years ago by
Colin
• 0
4
votes
3
replies
3.8k
views
clusterProfiler: Which GO version is used behind ?
clusterProfiler
updated 6.7 years ago by
Guido Hooiveld
★ 3.9k • written 6.7 years ago by
ZheFrench
▴ 50
0
votes
3
replies
3.8k
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
50 results • Page
1 of 1
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
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Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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