Showing : clusterprofiler • reset
0
votes
4
replies
105
views
error running enricher from clusterprofiler
clusterProfiler cluster
1 day ago Yael • 0
0
votes
1
reply
101
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 3 days ago by ★ 4.0k • written 4 days ago by • 0
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 23 days ago by 65k • written 23 days ago by ▴ 10
2
votes
13
replies
475
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
25 days ago • updated 22 days ago fernanda.backsouza ▴ 10
2
votes
2
replies
209
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 27 days ago by 65k • written 28 days ago by • 0
1
vote
2
replies
164
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
4 weeks ago Ana • 0
2
votes
2
replies
211
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
4 weeks ago julia_mcdonough • 0
0
votes
1
reply
192
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 4 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
votes
1
reply
187
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
0
votes
0
replies
161
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
5 weeks ago andromeda • 0
2
votes
1
reply
229
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 7 weeks ago by ★ 4.0k • written 7 weeks ago by ▴ 10
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 8 weeks ago by • 0 • written 6.4 years ago by ▴ 20
2
votes
2
replies
285
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
8 weeks ago Eva ▴ 10
1
vote
7
replies
1.6k
views
enrichGOgradient color change
clusterProfiler
updated 8 weeks ago by ★ 4.0k • written 6 months ago by • 0
1
vote
1
reply
208
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
15
replies
727
views
Problems with enrichGO
clusterProfiler enrichGO
updated 3 months ago by 42k • written 3 months ago by • 0
0
votes
3
replies
447
views
Unable to install clusterProfiler
clusterProfiler
updated 3 months ago by • 0 • written 3 months ago by • 0
0
votes
2
replies
350
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
3 months ago mello-vieira • 0
0
votes
1
reply
308
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
4
votes
2
replies
385
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
votes
3
replies
876
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 ★ 4.0k • written 5 months ago by • 0
3
votes
6
replies
2.2k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 19 months ago by ▴ 10
0
votes
9
replies
701
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago nromerov • 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
3
votes
4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
0
votes
2
replies
493
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
7 months ago georgii.vdovin • 0
0
votes
0
replies
385
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
7 months ago nromerov • 0
0
votes
2
replies
676
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
1
vote
2
replies
896
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
8 months ago fluentin44 • 0
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 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
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 9 months ago by • 0
0
votes
3
replies
1.5k
views
Not able to install clusterProfiler
clusterProfiler
updated 3 months ago by • 0 • written 10 months ago by • 0
0
votes
0
replies
358
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
10 months ago georgii.vdovin • 0
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
0
votes
1
reply
854
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 10 months ago by 65k • written 10 months ago by • 0
0
votes
5
replies
1.1k
views
plot enrichment results
enrichplot clusterProfiler
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
0
votes
2
replies
702
views
Question regarding FAQ
clusterProfiler
11 months ago kl-fr • 0
0
votes
0
replies
863
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
11 months ago pg45863 ▴ 10
2
votes
4
replies
1.6k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
11 months ago Tyroone • 0
0
votes
1
reply
1.1k
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
replies
1.4k
views
enrichKEGG function error
cluster clusterProfiler KEGG
13 months ago • updated 12 months ago ruba-mahmoud • 0
1
vote
3
replies
1.1k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 10
0
votes
1
reply
607
views
what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 13 months ago by 65k • written 13 months ago by ▴ 10
0
votes
3
replies
4.0k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 14 months ago by ★ 4.0k • written 15 months ago by • 0
0
votes
1
reply
1.2k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler enrichplot
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
1
vote
3
replies
886
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 22 days ago by ★ 1.2k • written 14 months ago by ▴ 10
4
votes
2
replies
4.5k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 14 months ago by ▴ 50 • written 14 months ago by • 0
1
vote
7
replies
1.9k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 4 months ago by ★ 4.0k • written 14 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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