Showing : clusterprofiler • reset
3
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4
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5.0k
views
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 9 weeks ago by 68k • written 11 weeks ago by ▴ 10
1
vote
3
replies
1.2k
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 4 months ago by 68k • written 4 months ago by • 0
0
votes
3
replies
1.2k
views
Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
4 months ago • updated 3 months ago GA ▴ 10
0
votes
1
reply
461
views
Error in cnetplot
enrichplot clusterProfiler
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
0
votes
1
reply
678
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
6 months ago Jessica • 0
0
votes
4
replies
862
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
7 months ago Quang NN ▴ 10
2
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2
replies
828
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 10 months ago by ★ 1.2k • written 10 months ago by • 0
7
votes
9
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1.8k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
0
votes
5
replies
1.3k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 11 months ago by ▴ 760 • written 12 months ago by • 0
1
vote
2
replies
2.9k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 12 months ago by • 0
0
votes
1
reply
1.2k
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
1
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5
replies
2.1k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 12 months ago by • 0
2
votes
4
replies
1.4k
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 12 months ago by 68k • written 12 months ago by • 0
1
vote
2
replies
794
views
Question on number of genes used in GO analysis
GO clusterProfiler
13 months ago Danté • 0
1
vote
1
reply
1.2k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
3
votes
1
reply
1.9k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 14 months ago by ★ 4.1k • written 14 months ago by ▴ 10
1
vote
2
replies
1.1k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
14 months ago sawa • 0
1
vote
9
replies
3.0k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 14 months ago by 68k • written 14 months ago by ▴ 10
0
votes
1
reply
779
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 14 months ago by 68k • written 14 months ago by • 0
8
votes
6
replies
8.5k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 15 months ago by ▴ 30 • written 6.3 years ago by ▴ 180
0
votes
4
replies
1.3k
views
error running enricher from clusterprofiler
clusterProfiler cluster
15 months ago Yael • 0
0
votes
1
reply
1.3k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
1
vote
1
reply
655
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 16 months ago by 68k • written 16 months ago by ▴ 30
5
votes
13
replies
3.6k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
16 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.4k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 16 months ago by 68k • written 16 months ago by • 0
1
vote
2
replies
2.4k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
16 months ago Ana • 0
2
votes
4
replies
2.1k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 16 months ago by • 0
0
votes
2
replies
2.4k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 13 days ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
560
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
0
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632
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
17 months ago andromeda • 0
2
votes
2
replies
1.3k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 17 months ago by ▴ 10
4
votes
4
replies
5.1k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 17 months ago by • 0 • written 7.7 years ago by ▴ 20
2
votes
2
replies
1.7k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
17 months ago Eva ▴ 10
3
votes
9
replies
7.5k
views
enrichGOgradient color change
clusterProfiler
updated 8 months ago by • 0 • written 21 months ago by • 0
1
vote
1
reply
647
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 18 months ago by 68k • written 18 months ago by • 0
2
votes
15
replies
2.4k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 18 months ago by 43k • written 19 months ago by • 0
0
votes
3
replies
1.5k
views
Unable to install clusterProfiler
clusterProfiler
updated 18 months ago by • 0 • written 19 months ago by • 0
0
votes
2
replies
1.3k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
19 months ago mello-vieira • 0
0
votes
1
reply
1.3k
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 19 months ago by 68k • written 19 months ago by • 0
4
votes
2
replies
1.2k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
0
votes
3
replies
2.3k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
3
votes
6
replies
4.2k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 21 months ago by 68k • written 2.9 years ago by ▴ 10
0
votes
9
replies
1.9k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
21 months ago nromerov • 0
2
votes
9
replies
3.4k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 22 months ago by ▴ 50 • written 22 months ago by ▴ 30
3
votes
4
replies
2.8k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
votes
2
replies
1.0k
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
23 months ago • updated 22 months ago georgii.vdovin • 0
0
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0
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833
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
23 months ago nromerov • 0
0
votes
2
replies
2.1k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 23 months ago by 68k • written 23 months ago by • 0
1
vote
2
replies
2.1k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
24 months ago fluentin44 • 0
0
votes
2
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3.3k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
2.0 years ago Valéria • 0
288 results • Page 1 of 6
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Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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