Showing : clusterProfiler • reset
0
votes
6
replies
8.6k
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
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 10 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
2
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2
replies
3.9k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 8 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 4 weeks ago by • 0 • written 6.4 years ago by ▴ 20
2
votes
5
replies
3.1k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
3
votes
6
replies
2.0k
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
2
replies
2.0k
views
clusterProfiler - custom annotations
clusterProfiler
updated 3 months ago by ★ 3.9k • written 16 months ago by • 0
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 13 months ago by ▴ 10
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
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
2
votes
4
replies
1.4k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
11 months ago • updated 10 months ago Tyroone • 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
1
vote
7
replies
1.4k
views
enrichGOgradient color change
clusterProfiler
updated 4 weeks ago by ★ 3.9k • written 5 months ago by • 0
0
votes
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
1.2k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 5 months ago by • 0 • written 8 months ago by • 0
2
votes
9
replies
1.1k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 5 months ago by ▴ 50 • written 5 months ago by ▴ 30
3
votes
4
replies
1.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 5 months ago by ★ 3.9k • written 5 months ago by • 0
0
votes
2
replies
1.1k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
7 months ago Valéria • 0
3
votes
2
replies
1.0k
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
1
reply
1.0k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 12 months ago by 3.8k • written 12 months ago by • 0
0
votes
5
replies
985
views
plot enrichment results
enrichplot clusterProfiler
updated 9 months ago by ▴ 730 • written 9 months ago by • 0
1
vote
2
replies
812
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
7 months ago fluentin44 • 0
0
votes
0
replies
807
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
10 months ago pg45863 ▴ 10
0
votes
3
replies
757
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
1
vote
2
replies
752
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 1 day ago by • 0 • written 13 months ago by ▴ 10
0
votes
1
reply
752
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
2
replies
655
views
Question regarding FAQ
clusterProfiler
10 months ago kl-fr • 0
2
votes
15
replies
632
views
Problems with enrichGO
clusterProfiler enrichGO
updated 9 weeks ago by 41k • written 10 weeks ago by • 0
0
votes
2
replies
603
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 6 months ago by 65k • written 6 months ago by • 0
0
votes
9
replies
602
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
4 months ago nromerov • 0
0
votes
2
replies
447
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
6 months ago georgii.vdovin • 0
0
votes
3
replies
376
views
Unable to install clusterProfiler
clusterProfiler
updated 9 weeks ago by • 0 • written 10 weeks ago by • 0
0
votes
0
replies
342
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
0
votes
0
replies
336
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
4
votes
2
replies
334
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
2
replies
287
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
10 weeks ago mello-vieira • 0
0
votes
1
reply
249
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
2
votes
2
replies
232
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
4 weeks ago Eva ▴ 10
2
votes
1
reply
177
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 26 days ago by ★ 3.9k • written 28 days ago by ▴ 10
1
vote
1
reply
173
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
2
votes
2
replies
150
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
7 days ago julia_mcdonough • 0
0
votes
1
reply
147
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 11 days ago by 65k • written 12 days ago by • 0
0
votes
0
replies
122
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
14 days ago andromeda • 0
0
votes
1
reply
115
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 5 days ago by ★ 3.9k • written 9 days ago by • 0
1
vote
2
replies
85
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
3 days ago Ana • 0
1
vote
2
replies
72
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 16 hours ago by 65k • written 1 day ago by • 0
47 results • Page 1 of 1
Recent ...
Replies
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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