Showing : ClusterProfiler • reset
1
vote
1
reply
53
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 1 day ago by 65k • written 1 day ago by ▴ 10
1
vote
13
replies
236
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
3 days ago • updated 4 hours ago fernanda.backsouza ▴ 10
2
votes
2
replies
137
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 5 days ago by 65k • written 6 days ago by • 0
1
vote
2
replies
110
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
8 days ago Ana • 0
2
votes
2
replies
165
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
12 days ago julia_mcdonough • 0
0
votes
1
reply
130
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 10 days ago by ★ 3.9k • written 14 days ago by • 0
0
votes
1
reply
159
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 16 days ago by 65k • written 17 days ago by • 0
0
votes
0
replies
129
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
19 days ago andromeda • 0
2
votes
1
reply
186
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 4 weeks ago by ★ 3.9k • written 4 weeks 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 5 weeks ago by • 0 • written 6.4 years ago by ▴ 20
2
votes
2
replies
240
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
5 weeks ago Eva ▴ 10
1
vote
7
replies
1.4k
views
enrichGOgradient color change
clusterProfiler
updated 5 weeks ago by ★ 3.9k • written 5 months ago by • 0
1
vote
1
reply
181
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
2
votes
15
replies
653
views
Problems with enrichGO
clusterProfiler enrichGO
updated 10 weeks ago by 41k • written 10 weeks ago by • 0
0
votes
3
replies
382
views
Unable to install clusterProfiler
clusterProfiler
updated 9 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
2
replies
297
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
11 weeks ago mello-vieira • 0
0
votes
1
reply
258
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
343
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
3
replies
775
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 4 months ago by ★ 3.9k • written 4 months ago by • 0
3
votes
6
replies
2.1k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 4 months ago by 65k • written 18 months ago by ▴ 10
0
votes
9
replies
622
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago • updated 4 months ago nromerov • 0
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 5 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 ★ 3.9k • written 6 months ago by • 0
0
votes
2
replies
452
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
6 months ago georgii.vdovin • 0
0
votes
0
replies
349
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
0
votes
2
replies
617
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
826
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
7 months ago fluentin44 • 0
0
votes
2
replies
1.1k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
8 months ago • updated 7 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
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
0
votes
3
replies
1.4k
views
Not able to install clusterProfiler
clusterProfiler
updated 9 weeks ago by • 0 • written 9 months ago by • 0
0
votes
0
replies
339
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
2
votes
5
replies
3.1k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
0
votes
1
reply
777
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
0
votes
5
replies
1.0k
views
plot enrichment results
enrichplot clusterProfiler
updated 9 months ago by ▴ 730 • written 10 months ago by • 0
0
votes
2
replies
671
views
Question regarding FAQ
clusterProfiler
10 months ago kl-fr • 0
0
votes
0
replies
815
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
11 months ago pg45863 ▴ 10
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
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
12 months ago • updated 11 months ago ruba-mahmoud • 0
1
vote
3
replies
809
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 15 hours ago by ★ 1.2k • written 13 months ago by ▴ 10
2
votes
6
replies
1.9k
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
0
votes
2
replies
2.1k
views
clusterProfiler - custom annotations
clusterProfiler
updated 3 months ago by ★ 3.9k • written 16 months ago by • 0
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 9 weeks ago by • 0 • written 22 months ago by • 0
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 11 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
3
votes
3
replies
4.6k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
0
votes
1
reply
1.5k
views
ClusterProfiler - enrichKEGG on specific pathways
kegg enrichkegg clusterprofiler
updated 4 months ago by • 0 • written 5.7 years ago by ▴ 40
0
votes
6
replies
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
2
votes
2
replies
3.9k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 9 months ago by • 0 • written 7.8 years ago by ▴ 10
48 results • Page 1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Scholar to ATpoint ★ 4.0k
Locations • All
WEHI, Melbourne, Australia, 12 minutes ago
France, 18 minutes ago
Melbourne, Australia, 21 minutes ago
United States, 25 minutes ago
Canada, 1 hour ago
Traffic: 760 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6