Showing : ClusterProfiler • reset
0
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6
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8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler r
updated 3 months ago by ★ 3.9k • written 7.3 years ago by • 0
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 12 weeks ago by ★ 3.9k • written 3.3 years ago by • 0
3
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3
replies
4.7k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
2
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2
replies
4.0k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 9 months ago by • 0 • written 7.8 years ago by ▴ 10
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 6 weeks ago by • 0 • written 6.4 years ago by ▴ 20
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
3
votes
6
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2.1k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 18 months ago by ▴ 10
0
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2
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2.1k
views
clusterProfiler - custom annotations
clusterProfiler
updated 3 months ago by ★ 3.9k • written 16 months ago by • 0
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 3 months ago by ★ 3.9k • written 14 months ago by ▴ 10
1
vote
3
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1.9k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 11 weeks ago by • 0 • written 23 months ago by • 0
0
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1
reply
1.5k
views
ClusterProfiler - enrichKEGG on specific pathways
kegg enrichkegg clusterprofiler
updated 5 months ago by • 0 • written 5.8 years ago by ▴ 40
2
votes
4
replies
1.5k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
11 months ago Tyroone • 0
1
vote
7
replies
1.5k
views
enrichGOgradient color change
clusterProfiler
updated 6 weeks ago by ★ 3.9k • written 5 months ago by • 0
0
votes
3
replies
1.5k
views
Not able to install clusterProfiler
clusterProfiler
updated 11 weeks ago by • 0 • written 9 months ago by • 0
0
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5
replies
1.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
12 months ago • updated 11 months ago ruba-mahmoud • 0
0
votes
3
replies
1.3k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 6 months ago by • 0 • written 8 months ago by • 0
3
votes
4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 3.9k • written 6 months ago by • 0
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 6 months ago by ▴ 50 • written 6 months ago by ▴ 30
0
votes
2
replies
1.2k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
8 months ago Valéria • 0
3
votes
2
replies
1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
0
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5
replies
1.0k
views
plot enrichment results
enrichplot clusterProfiler
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
1
vote
2
replies
862
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
7 months ago fluentin44 • 0
1
vote
3
replies
857
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 10 days ago by ★ 1.2k • written 14 months ago by ▴ 10
0
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0
replies
839
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
11 months ago pg45863 ▴ 10
0
votes
3
replies
817
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 5 months ago by ★ 3.9k • written 5 months ago by • 0
0
votes
1
reply
808
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 9 months ago by 65k • written 9 months ago by • 0
2
votes
15
replies
698
views
Problems with enrichGO
clusterProfiler enrichGO
updated 11 weeks ago by 41k • written 12 weeks ago by • 0
0
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2
replies
690
views
Question regarding FAQ
clusterProfiler
10 months ago kl-fr • 0
0
votes
9
replies
660
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago nromerov • 0
0
votes
2
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647
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 7 months ago by 65k • written 7 months ago by • 0
0
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2
replies
472
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
6 months ago georgii.vdovin • 0
0
votes
3
replies
417
views
Unable to install clusterProfiler
clusterProfiler
updated 11 weeks ago by • 0 • written 12 weeks ago by • 0
1
vote
13
replies
395
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
13 days ago • updated 10 days ago fernanda.backsouza ▴ 10
0
votes
0
replies
369
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
4
votes
2
replies
363
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
0
votes
0
replies
354
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
0
votes
2
replies
318
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
3 months ago • updated 12 weeks ago mello-vieira • 0
0
votes
1
reply
274
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
2
replies
259
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
6 weeks ago Eva ▴ 10
2
votes
1
reply
211
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 5 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
1
vote
1
reply
199
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
2
votes
2
replies
191
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
22 days ago julia_mcdonough • 0
2
votes
2
replies
186
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 15 days ago by 65k • written 16 days ago by • 0
0
votes
1
reply
180
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 26 days ago by 65k • written 27 days ago by • 0
0
votes
1
reply
157
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 20 days ago by ★ 3.9k • written 24 days ago by • 0
0
votes
0
replies
143
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
29 days ago andromeda • 0
1
vote
2
replies
137
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
18 days ago Ana • 0
1
vote
1
reply
109
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 11 days ago by 65k • written 11 days ago by ▴ 10
48 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
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Comment: Too many significant genes when integrating gtex and tcga
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