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Showing :
clusterprofiler
•
reset
0
votes
0
replies
43
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
3 days ago • updated 2 days ago
pg45863
• 0
2
votes
4
replies
121
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot
clusterProfiler
7 days ago • updated 6 days ago
Tyroone
• 0
0
votes
1
reply
141
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler
AnnotationForge
updated 5 weeks ago by
shepherl
3.5k • written 5 weeks ago by
yuwt8920
• 0
0
votes
5
replies
255
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
6 weeks ago • updated 20 days ago
ruba-mahmoud
• 0
1
vote
3
replies
214
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 7 weeks ago by
Guido Hooiveld
★ 3.6k • written 8 weeks ago by
m-bihie
▴ 10
0
votes
1
reply
126
views
what does "exp1" mean in the gage() function?
gage
clusterProfiler
DESeq2
updated 9 weeks ago by
James W. MacDonald
63k • written 9 weeks ago by
m-bihie
▴ 10
0
votes
3
replies
511
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 11 weeks ago by
Guido Hooiveld
★ 3.6k • written 3 months ago by
YNKIM
• 0
0
votes
1
reply
171
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler
enrichplot
updated 10 weeks ago by
Guido Hooiveld
★ 3.6k • written 11 weeks ago by
GenoMexa
• 0
0
votes
1
reply
163
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 12 weeks ago by
ATpoint
★ 2.9k • written 12 weeks ago by
ruiqi.li
• 0
4
votes
2
replies
1.2k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 3 months ago by
Erqiang Hu
▴ 50 • written 3 months ago by
redafazazi
• 0
1
vote
7
replies
495
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 3 months ago by
Basti
▴ 720 • written 3 months ago by
ruiqi.li
• 0
1
vote
4
replies
386
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
3 months ago
ruiqi.li
• 0
0
votes
1
reply
254
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 4 months ago by
Michael Love
40k • written 4 months ago by
joanna
• 0
0
votes
1
reply
411
views
clusterProfiler - custom annotations
clusterProfiler
updated 5 months ago by
Guido Hooiveld
★ 3.6k • written 5 months ago by
adam
• 0
1
vote
1
reply
350
views
How to include background "universe" in compareCluster function of clusterprofiler package
clusterProfiler
updated 5 months ago by
Basti
▴ 720 • written 5 months ago by
ghs101
• 0
1
vote
7
replies
629
views
Adding geneID to list of gene locus IDs
cluster
OrgDb
clusterProfiler
written 6 months ago by
Chruut
• 0
2
votes
4
replies
787
views
question regarding installation of "enrichplot" with BiocManager
R
BiocManager
install
clusterProfiler
GO
written 6 months ago by
abhisek001
• 0
7
votes
6
replies
656
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 5 months ago by
Gordon Smyth
47k • written 5 months ago by
nhaus
• 0
0
votes
2
replies
1.9k
views
Error in UseMethod("rescale")
clusterProfiler
updated 5 months ago by
Guido Hooiveld
★ 3.6k • written 5 months ago by
vvelagal
• 0
0
votes
7
replies
896
views
Mouse GSEA Analysis
clusterProfiler
updated 6 months ago by
Michael Love
40k • written 6 months ago by
Rob
• 0
0
votes
0
replies
269
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
6 months ago
Rob
• 0
1
vote
9
replies
653
views
Why is OrgDb linked to specific biocversion? / How to analyze old datasets?
BiocVersion
OrgDb
clusterProfiler
7 months ago • updated 6 months ago
MK
• 0
0
votes
0
replies
226
views
How to perform a cluster analysis in RT-qPCR or HT-qPCR results?
cluster
qpcr
qpcrNorm
clusterProfiler
HTqPCR
7 months ago
Javier
• 0
0
votes
0
replies
179
views
Over Representation Analysis using PFAM/InterPro database
PFAM.db
clusterProfiler
7 months ago
alexandr.gopanenko
▴ 40
0
votes
4
replies
354
views
Error installing Bioc
clusterProfiler
Bioconductor
BiocManager
updated 7 months ago by
Guido Hooiveld
★ 3.6k • written 7 months ago by
Javier
• 0
2
votes
4
replies
675
views
Result from GSEA for non-model organism not as expected
clusterProfiler
7 months ago
Susanne
• 0
4
votes
4
replies
2.7k
views
Clarifications on p-values in enrichResult objects
clusterProfiler
reactomepa
dose
updated 7 months ago by
12133067
• 0 • written 6.8 years ago by
enricoferrero
▴ 660
0
votes
1
reply
854
views
Cannot install package "clusterProfiler" by BiocManager::install()
clusterProfiler
BiocManager
updated 7 months ago by
shepherl
3.5k • written 7 months ago by
xqhuqd
• 0
1
vote
2
replies
367
views
bitr returning unexpected length of gene IDs after conversion.
clusterProfiler
updated 8 months ago by
James W. MacDonald
63k • written 8 months ago by
quoc.t.nguyen96
• 0
2
votes
3
replies
914
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi
GO
clusterProfiler
enrichplot
ensembldb
updated 8 months ago by
merv
▴ 60 • written 8 months ago by
simone.nevills
▴ 10
0
votes
1
reply
616
views
Treeplot by enrichplot
clusterProfiler
enrichplot
treeplot
updated 7 months ago by
Guangchuang Yu
★ 1.2k • written 8 months ago by
g.neri19
• 0
0
votes
0
replies
314
views
Simplify - clusterProfiler
RNASeq
simplify
clusterProfiler
enrichGO
simplifyEnrichment
8 months ago
estafana.t98
• 0
1
vote
2
replies
1.8k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler
DOSE
updated 5 months ago by
Nick O
• 0 • written 8 months ago by
ummscr
• 0
4
votes
6
replies
1.8k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 9 months ago by
Guido Hooiveld
★ 3.6k • written 11 months ago by
rama
▴ 10
3
votes
5
replies
1.5k
views
how to color specific node or gene symbol from cnetplot ?
clusterProfiler
enrichplot
cnetplot
GuangchuangYu
updated 9 months ago by
Guangchuang Yu
★ 1.2k • written 12 months ago by
adR
▴ 30
0
votes
0
replies
331
views
Cluster profiler - adj p-value differ from Enrichr
clusterProfiler
enrichR
9 months ago
angkoo
▴ 10
1
vote
1
reply
740
views
How should I set my eps value in cluster profiler?
clusterProfiler
updated 9 months ago by
Guido Hooiveld
★ 3.6k • written 9 months ago by
ummscr
• 0
1
vote
1
reply
350
views
GSEA with Wikipathways not entirely reproducible
clusterProfiler
updated 9 months ago by
Guido Hooiveld
★ 3.6k • written 9 months ago by
Susana
• 0
0
votes
3
replies
2.2k
views
ridgeplot doesn't work: Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero
clusterProfiler
updated 7 months ago by
mttrantrietminh
• 0 • written 10 months ago by
Y.K
• 0
0
votes
1
reply
601
views
setReadable function missing information in clusterProfiler
clusterProfiler
updated 10 months ago by
James W. MacDonald
63k • written 10 months ago by
ltb47
• 0
1
vote
1
reply
719
views
enrichGO results
clusterProfiler
enrichGO
10 months ago
Shakiba
• 0
0
votes
3
replies
1.5k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler
enrichplot
clusterpro
doseR
dose
updated 10 months ago by
Guido Hooiveld
★ 3.6k • written 11 months ago by
rama
▴ 10
0
votes
4
replies
609
views
how to get the gene set from online GO database
clusterProfiler
WebGestalR
11 months ago • updated 10 months ago
pengmin.wang.1
• 0
1
vote
2
replies
3.5k
views
ENSEMBL to ENTREZ ID
clusterProfiler
11 months ago
martacrespi7
• 0
0
votes
1
reply
472
views
Dotplot from enricher outputting very few genes
clusterProfiler
enrichplot
updated 11 months ago by
Guido Hooiveld
★ 3.6k • written 11 months ago by
Lucía
▴ 10
0
votes
2
replies
854
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 9 weeks ago by
Aciole.D
• 0 • written 11 months ago by
AP
• 0
0
votes
1
reply
763
views
TERM2NAME for enricher if I have list of GO IDs
clusterProfiler
GO.db
12 months ago
Lucía
▴ 10
0
votes
5
replies
925
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler
goseq
topGO
DESeq2
updated 12 months ago by
James W. MacDonald
63k • written 12 months ago by
Lucía
▴ 10
0
votes
0
replies
293
views
Not obtaining significant Gene Ontology Biological Process hits
clusterProfiler
12 months ago
Jordan
• 0
0
votes
13
replies
1.5k
views
EnrichGO not working with db created from annotationhub
clusterProfiler
AnnotationHubData
GO
updated 12 months ago by
Guido Hooiveld
★ 3.6k • written 12 months ago by
Lucía
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Error: biomaRt has encountered an unexpected server error.
by
Mike Smith
★ 6.0k
Unfortunately, the BioMart LDS functionality have been flaky for a while now e.g. https://support.bioconductor.org/p/9143401/ , https:/…
Comment: Use with_go along with other filters in getBM function
by
Mike Smith
★ 6.0k
Hi @rubbit0, I'm not sure I understand what you're trying to do. Do you have a long list of Ensembl Gene IDs and you're trying to select …
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Anna
▴ 20
Dear Gordon, these are my metadata. As you see some subject are missing for timepoint 1 Subject Timepoint 1 ID1 Baselin…
Comment: Question on constructing design matrix and defining contrasts for analysis
by
mohammedtoufiq91
▴ 10
Sure, noted.
Comment: Question on constructing design matrix and defining contrasts for analysis
by
mohammedtoufiq91
▴ 10
@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …
Votes
Dispersion plot -Interpretation -DESeq2
Answer: Dispersion Estimates and MA plots
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
WGCNA coupled with differential expression analysis: question about baseline module detection
WGCNA with paired samples
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