Showing : ClusterProfiler • reset
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GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
updated 11 hours ago by 66k • written 12 hours ago by • 0
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3
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73
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 1 day ago by 66k • written 1 day ago by • 0
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1
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42
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How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 1 day ago by 66k • written 1 day ago by • 0
8
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6
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4.4k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 21 days ago by ▴ 30 • written 5.1 years ago by ▴ 160
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4
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229
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error running enricher from clusterprofiler
clusterProfiler cluster
29 days ago Yael • 0
0
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1
reply
265
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 4 weeks ago by ★ 4.0k • written 4 weeks ago by • 0
1
vote
1
reply
156
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 7 weeks ago by 66k • written 7 weeks ago by ▴ 10
2
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13
replies
692
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
7 weeks ago fernanda.backsouza ▴ 10
2
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2
replies
280
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 7 weeks ago by 66k • written 8 weeks ago by • 0
1
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2
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236
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
8 weeks ago Ana • 0
2
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2
replies
266
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
8 weeks ago julia_mcdonough • 0
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1
reply
272
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 8 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
0
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1
reply
215
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 9 weeks ago by 66k • written 9 weeks ago by • 0
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0
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184
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
9 weeks ago andromeda • 0
2
votes
1
reply
289
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 11 weeks ago by ★ 4.0k • written 11 weeks ago by ▴ 10
4
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4
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3.9k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 12 weeks ago by • 0 • written 6.5 years ago by ▴ 20
2
votes
2
replies
363
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
12 weeks ago Eva ▴ 10
1
vote
8
replies
2.1k
views
enrichGOgradient color change
clusterProfiler
updated 21 days ago by • 0 • written 7 months ago by • 0
1
vote
1
reply
236
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 3 months ago by 66k • written 3 months ago by • 0
2
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15
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799
views
Problems with enrichGO
clusterProfiler enrichGO
updated 4 months ago by 42k • written 4 months ago by • 0
0
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3
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531
views
Unable to install clusterProfiler
clusterProfiler
updated 3 months ago by • 0 • written 4 months ago by • 0
0
votes
2
replies
441
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
4 months ago mello-vieira • 0
0
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1
reply
390
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 4 months ago by 66k • written 4 months ago by • 0
4
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2
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454
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
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3
replies
994
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
3
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6
replies
2.3k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 6 months ago by 66k • written 19 months ago by ▴ 10
0
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9
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803
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
6 months ago nromerov • 0
2
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9
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1.8k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 7 months ago by ▴ 50 • written 7 months ago by ▴ 30
3
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4
replies
1.3k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
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2
replies
542
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
8 months ago • updated 7 months ago georgii.vdovin • 0
0
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0
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413
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
8 months ago nromerov • 0
0
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2
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808
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 8 months ago by 66k • written 8 months ago by • 0
1
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2
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1.0k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
9 months ago fluentin44 • 0
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2
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1.4k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
9 months ago Valéria • 0
3
votes
2
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1.2k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
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3
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1.5k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 7 months ago by • 0 • written 10 months ago by • 0
0
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3
replies
1.6k
views
Not able to install clusterProfiler
clusterProfiler
updated 3 months ago by • 0 • written 10 months ago by • 0
0
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0
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381
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
11 months ago georgii.vdovin • 0
2
votes
5
replies
3.3k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.4 years ago by • 0
0
votes
1
reply
960
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 11 months ago by 66k • written 11 months ago by • 0
0
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5
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1.1k
views
plot enrichment results
enrichplot clusterProfiler
updated 11 months ago by ▴ 730 • written 11 months ago by • 0
0
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2
replies
740
views
Question regarding FAQ
clusterProfiler
12 months ago • updated 11 months ago kl-fr • 0
0
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0
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939
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
12 months ago pg45863 ▴ 10
2
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4
replies
1.7k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
12 months ago Tyroone • 0
0
votes
1
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1.2k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 13 months ago by 3.9k • written 13 months ago by • 0
0
votes
5
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1.4k
views
enrichKEGG function error
cluster clusterProfiler KEGG
14 months ago • updated 13 months ago ruba-mahmoud • 0
1
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3
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1.2k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 14 months ago by ★ 4.0k • written 14 months ago by ▴ 10
0
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1
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637
views
what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 14 months ago by 66k • written 14 months ago by ▴ 10
1
vote
3
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4.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 15 months ago by ★ 4.0k • written 16 months ago by ▴ 10
0
votes
1
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1.3k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler enrichplot
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
50 results • Page 1 of 1
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for looking into this and for your explanation! As a follow-up, would it be possible in future releases of featureCounts to pro…
Comment: error loading collectTRI regulon by silvaesilva.da • 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate by James W. MacDonald 66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Answer: Limma model.matrix design with batch effect and different life stages proportion by Masongeorge • 0
Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.
Comment: error loading collectTRI regulon by deeenes ▴ 50
I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…
Votes
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Answer: DESeq2 returns results for group with just one replicate
Answer: DESeq2 returns results for group with just one replicate
Comment: error loading collectTRI regulon
A: Scaling option in fastMNN
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