Showing : clusterProfiler • reset
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
8 days ago • updated 6 days ago Quang NN ▴ 10
2
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2
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468
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 3 months ago by ★ 1.2k • written 3 months ago by • 0
7
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9
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1.3k
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clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
5
replies
802
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 4 months ago by ▴ 760 • written 4 months ago by • 0
1
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2
replies
1.4k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 4 months ago by • 0
0
votes
1
reply
621
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 4 months ago by ★ 4.1k • written 5 months ago by • 0
1
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5
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1.3k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 5 months ago by • 0
2
votes
4
replies
906
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 5 months ago by 67k • written 5 months ago by • 0
1
vote
2
replies
453
views
Question on number of genes used in GO analysis
GO clusterProfiler
5 months ago Danté • 0
1
vote
1
reply
625
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 6 months ago by ★ 4.1k • written 6 months ago by • 0
3
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1
reply
1.2k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 7 months ago by ★ 4.1k • written 7 months ago by ▴ 10
1
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2
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763
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
7 months ago sawa • 0
1
vote
9
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1.7k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 7 months ago by 67k • written 7 months ago by ▴ 10
0
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1
reply
486
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 7 months ago by 67k • written 7 months ago by • 0
8
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6
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6.5k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 8 months ago by ▴ 30 • written 5.7 years ago by ▴ 160
0
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4
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746
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error running enricher from clusterprofiler
clusterProfiler cluster
8 months ago Yael • 0
0
votes
1
reply
836
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
vote
1
reply
414
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 9 months ago by 67k • written 9 months ago by ▴ 30
5
votes
13
replies
2.4k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
9 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
866
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 9 months ago by 67k • written 9 months ago by • 0
1
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2
replies
1.4k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
9 months ago Ana • 0
2
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3
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1.0k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 11 weeks ago by • 0 • written 9 months ago by • 0
0
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1
reply
1.4k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
0
votes
1
reply
424
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 9 months ago by 67k • written 9 months ago by • 0
0
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0
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455
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
9 months ago andromeda • 0
2
votes
2
replies
871
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 10 months ago by ▴ 10
4
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4
replies
4.5k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 10 months ago by • 0 • written 7.1 years ago by ▴ 20
2
votes
2
replies
1.1k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
10 months ago Eva ▴ 10
2
votes
9
replies
5.0k
views
enrichGOgradient color change
clusterProfiler
updated 27 days ago by • 0 • written 14 months ago by • 0
1
vote
1
reply
460
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 11 months ago by 67k • written 11 months ago by • 0
2
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15
replies
1.6k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 11 months ago by 43k • written 11 months ago by • 0
0
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3
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1.1k
views
Unable to install clusterProfiler
clusterProfiler
updated 11 months ago by • 0 • written 11 months ago by • 0
0
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2
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916
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
12 months ago • updated 11 months ago mello-vieira • 0
0
votes
1
reply
858
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 12 months ago by 67k • written 12 months ago by • 0
4
votes
2
replies
891
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
votes
3
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1.9k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
3
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6
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3.3k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 14 months ago by 67k • written 2.3 years ago by ▴ 10
0
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9
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1.4k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
14 months ago nromerov • 0
2
votes
9
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3.0k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 15 months ago by ▴ 50 • written 15 months ago by ▴ 30
3
votes
4
replies
2.0k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
0
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2
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825
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
15 months ago georgii.vdovin • 0
0
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0
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656
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
15 months ago nromerov • 0
0
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2
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1.5k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 16 months ago by 67k • written 16 months ago by • 0
1
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2
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1.6k
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Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
16 months ago fluentin44 • 0
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2
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2.4k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
17 months ago Valéria • 0
3
votes
2
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2.0k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 17 months ago by ★ 4.1k • written 17 months ago by ▴ 10
0
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3
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2.3k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 15 months ago by • 0 • written 17 months ago by • 0
0
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3
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2.7k
views
Not able to install clusterProfiler
clusterProfiler
updated 11 months ago by • 0 • written 18 months ago by • 0
0
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0
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564
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
18 months ago georgii.vdovin • 0
2
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5
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3.9k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 4.0 years ago by • 0
50 results • Page 1 of 1
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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