Showing : clusterProfiler • reset
0
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188
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Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
updated 1 day ago by 68k • written 3 days ago by ▴ 10
0
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1
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255
views
Error in cnetplot
enrichplot clusterProfiler
updated 28 days ago by ★ 4.1k • written 4 weeks ago by • 0
0
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1
reply
260
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
10 weeks ago Jessica • 0
0
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4
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653
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
3 months ago Quang NN ▴ 10
2
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2
replies
664
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 5 months ago by ★ 1.2k • written 6 months ago by • 0
7
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9
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1.5k
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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 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
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5
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1.1k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 7 months ago by ▴ 760 • written 7 months ago by • 0
1
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2
replies
2.3k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 7 months ago by • 0
0
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1
reply
925
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
1
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5
replies
1.7k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 8 months ago by • 0
2
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4
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1.2k
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 7 months ago by 68k • written 8 months ago by • 0
1
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2
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622
views
Question on number of genes used in GO analysis
GO clusterProfiler
8 months ago Danté • 0
1
vote
1
reply
965
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
3
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1
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1.6k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
1
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2
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955
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
10 months ago sawa • 0
1
vote
9
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2.5k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 10 months ago by 68k • written 10 months ago by ▴ 10
0
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1
reply
667
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 10 months ago by 68k • written 10 months ago by • 0
8
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6
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7.8k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 11 months ago by ▴ 30 • written 6.0 years ago by ▴ 180
0
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4
replies
1.1k
views
error running enricher from clusterprofiler
clusterProfiler cluster
11 months ago Yael • 0
0
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1
reply
1.1k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
1
vote
1
reply
490
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 12 months ago by 68k • written 12 months ago by ▴ 30
5
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13
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3.1k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
12 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.1k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 12 months ago by 68k • written 12 months ago by • 0
1
vote
2
replies
1.8k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
12 months ago Ana • 0
2
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4
replies
1.7k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 12 months ago by • 0
0
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1
reply
1.9k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
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1
reply
489
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 12 months ago by 68k • written 12 months ago by • 0
0
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0
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537
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
12 months ago andromeda • 0
2
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2
replies
1.1k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 13 months ago by ▴ 10
4
votes
4
replies
4.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 13 months ago by • 0 • written 7.4 years ago by ▴ 20
2
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2
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1.4k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
13 months ago Eva ▴ 10
3
votes
9
replies
6.4k
views
enrichGOgradient color change
clusterProfiler
updated 3 months ago by • 0 • written 17 months ago by • 0
1
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1
reply
541
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 14 months ago by 68k • written 14 months ago by • 0
2
votes
15
replies
2.0k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 14 months ago by 43k • written 14 months ago by • 0
0
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3
replies
1.3k
views
Unable to install clusterProfiler
clusterProfiler
updated 14 months ago by • 0 • written 14 months ago by • 0
0
votes
2
replies
1.1k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
14 months ago mello-vieira • 0
0
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1
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1.1k
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 15 months ago by 68k • written 15 months ago by • 0
4
votes
2
replies
1.0k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
0
votes
3
replies
2.1k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 16 months ago by ★ 4.1k • written 17 months ago by • 0
3
votes
6
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3.8k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 17 months ago by 68k • written 2.5 years ago by ▴ 10
0
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9
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1.6k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
17 months ago nromerov • 0
2
votes
9
replies
3.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 18 months ago by ▴ 50 • written 18 months ago by ▴ 30
3
votes
4
replies
2.4k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
0
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2
replies
898
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
18 months ago georgii.vdovin • 0
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0
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752
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
18 months ago nromerov • 0
0
votes
2
replies
1.8k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 19 months ago by 68k • written 19 months ago by • 0
1
vote
2
replies
1.8k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
19 months ago fluentin44 • 0
0
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2
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2.9k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
20 months ago Valéria • 0
3
votes
2
replies
2.4k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 20 months ago by ★ 4.1k • written 20 months ago by ▴ 10
0
votes
3
replies
2.7k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 18 months ago by • 0 • written 20 months ago by • 0
50 results • Page 1 of 1
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Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Votes
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
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